ecoblender

alex.filazzola

Abstract

Shrubs facilitate the abundance and productive of annual plants in desert ecosystems.However, these shrub microhabitats favour plant species with competitive life histories. Ephedra californica is a dominant shrub in the San Joaquin desert that has been identified as a facilitator. Here, we explore the factors that limit the Ephedra californica recruitment into the San Joaquin desert including substrate, water availability, and herbivory. We also explore the role of the invasive grass Bromus madritensis on limiting establishment of E. californica. Vegetation surveys were conducted in the field during 2013 and collected seed was then used to conduct two greenhouse trials. The first explore germination and establishment techniques for E. california and the optimal substrate. The second examined E. californica establishment in present of the invasive B. madritensis responding to different water levels and herbivory. These results can have implications for land managers in the San Joaquin Valley to maintain native shrub biodiversity in the region.


## load libraries
library(tidyverse)
# library(OIsurv)
library(lsmeans)
library(ggthemes)
library(ape)

## load data
substrate <-read.csv("data/Ephedra.substrate.csv")
recruit <-read.csv("data/Ephedra.recruitment.csv")
landscape <-read.csv("data/ephedra.landscape.csv")

##load functions
## inverse hyperbolic sine transformation 
ihs <- function(x) {
    y <- log(x + sqrt(x ^ 2 + 1))
    return(y)
}
se <- function(x, ...) sqrt(var(na.omit(x))/length(na.omit(x)))
source("functions.r")

Ephedra characteristics at the landscape

avg.size <- landscape %>% summarize(h=mean(H), d1=mean(D1), area=mean(Area), density=mean(Shrub.density), rdm=mean(RDM.2013),h.se=se(H), d1.se=se(D1), area.se=se(Area), density.se=se(Shrub.density), rdm.se=se(RDM.2013))
avg.size
##          h       d1     area     density      rdm       h.se      d1.se
## 1 1.332925 3.446412 9.321902 0.004318859 7.042223 0.01506635 0.05137079
##     area.se   density.se    rdm.se
## 1 0.2708882 6.272347e-05 0.2109119

Ephedra recruitment at landscape

## compare ephedra size and density across landscape
landscape[,"area.group"] <- as.numeric(cut(landscape$Log.area,20))
hist(landscape$area.group)

mean.area <- landscape %>% group_by(area.group) %>%  summarize(rdm=mean(RDM.2013), area=mean(Log.area), density=mean(Shrub.density))

ggplot(mean.area) + geom_point(aes(x=density, y=area), size=3)+ylab("log (area of shrub)")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16)) + xlab(expression("shrub density (m"^"2"*")")) +  stat_smooth(method="lm", formula= y~x,aes(x=density, y=area))

m1 <- lm(area~density, data=mean.area)
summary(m1)
## 
## Call:
## lm(formula = area ~ density, data = mean.area)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -0.82510 -0.26068  0.01197  0.22216  1.16732 
## 
## Coefficients:
##               Estimate Std. Error t value Pr(>|t|)    
## (Intercept)     9.3959     0.9852   9.537 1.84e-08 ***
## density     -1706.0323   223.6888  -7.627 4.81e-07 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.5569 on 18 degrees of freedom
## Multiple R-squared:  0.7637, Adjusted R-squared:  0.7506 
## F-statistic: 58.17 on 1 and 18 DF,  p-value: 4.806e-07
## convert RDM to kg

ggplot(mean.area) + geom_point(aes(x=rdm*20, y=density), size=mean.area$area+1)+xlab("residual dry matter (kg / acre)")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16)) + ylab(expression("shrub density (m"^"2"*")")) +  stat_smooth(method="lm", formula= y~x,aes(x=rdm*20, y=density))

m2 <- lm(log(rdm)~density, data=mean.area)
summary(m2)
## 
## Call:
## lm(formula = log(rdm) ~ density, data = mean.area)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -0.32696 -0.09127 -0.02044  0.05849  0.46804 
## 
## Coefficients:
##              Estimate Std. Error t value Pr(>|t|)    
## (Intercept)    3.1851     0.3294   9.670 1.49e-08 ***
## density     -279.3744    74.7892  -3.735  0.00151 ** 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.1862 on 18 degrees of freedom
## Multiple R-squared:  0.4367, Adjusted R-squared:  0.4054 
## F-statistic: 13.95 on 1 and 18 DF,  p-value: 0.001514
m1 <- lm(Shrub.density ~ RDM.2013, data=landscape) ## compare RDM with shrub density 

m3 <- manova(cbind(Shrub.density, Log.area) ~ RDM.2013, data=landscape)
summary(m3)
##            Df   Pillai approx F num Df den Df   Pr(>F)    
## RDM.2013    1 0.028461   10.121      2    691 4.65e-05 ***
## Residuals 692                                             
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
summary.aov(m3)
##  Response Shrub.density :
##              Df     Sum Sq    Mean Sq F value Pr(>F)
## RDM.2013      1 0.00000172 1.7228e-06  0.6307 0.4274
## Residuals   692 0.00189042 2.7318e-06               
## 
##  Response Log.area :
##              Df Sum Sq Mean Sq F value    Pr(>F)    
## RDM.2013      1   9.50  9.5046  17.183 3.815e-05 ***
## Residuals   692 382.77  0.5531                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Ephedra optimal substrate

substrate[,"Sand"] <- as.factor(substrate$Sand)
substrate[,"census"] <- as.factor(substrate$census)

m1 <- aov(height ~ Micro * Sand,  data=subset(substrate, census==10))
summary(m2) ## nothing significant


## compare shade on survival of ephedra
my.surv <- Surv(as.numeric(substrate$census), substrate$survival)
fit1 <- survfit(my.surv~Micro, data=substrate)
summary(fit1)


par(mar=c(4.5,4.5,.5,.5))
plot(fit1, col="white", ylim=c(0.2,1), xlim=c(0.9,10.1), ylab="Estimated Survival Function", xlab="Census", cex.lab=1.5, cex.axis=1.3)
lines(1:10,summary(fit1)[[10]][1:10], col="#E69F00", lty=2) ## upper
lines(1:10,summary(fit1)[[6]][1:10], col="#E69F00", lwd=2) ## value sun
lines(1:10,summary(fit1)[[11]][1:10], col="#E69F00", lty=2) ## lower
lines(1:10,summary(fit1)[[10]][11:20], col="#56B4E9", lty=2) ## upper
lines(1:10,summary(fit1)[[6]][11:20], col="#56B4E9", lwd=2) ## value shade
lines(1:10,summary(fit1)[[11]][11:20], col="#56B4E9", lty=2) ## lower
legend(1.8, 0.35, c("Sun","Shade"), lty=1, lwd=3, col=c("#E69F00","#56B4E9"), cex=1.5)

coxph.fit <- coxph(my.surv ~ Micro, method="breslow", data=substrate)
coxph.fit 


## compare sand on survival of ephedra
my.surv <- Surv(as.numeric(substrate$census), substrate$survival)
fit2 <- survfit(my.surv~Sand, data=substrate)
summary(fit2)


test <- substrate %>% group_by(census,Sand) %>%  summarize(count=sum(survival),avg=mean(survival))
test <- data.frame(test)

par(mar=c(4.5,4.5,.5,.5))
plot(fit2, col="white", ylim=c(0.2,1), xlim=c(0.9,10.1), ylab="Estimated Survival Function", xlab="Census", cex.lab=1.5, cex.axis=1.3)
lines(1:10,summary(fit2)[[10]][1:10], col="#E69F00", lty=2) ## upper
lines(1:10,summary(fit2)[[6]][1:10], col="#E69F00", lwd=2) ## value sand 0
lines(1:10,summary(fit2)[[11]][1:10], col="#E69F00", lty=2) ## lower
lines(1:10,summary(fit2)[[10]][11:20], col="#56B4E9", lty=2) ## upper
lines(1:10,summary(fit2)[[6]][11:20], col="#56B4E9", lwd=2) ## value sand 25
lines(1:10,summary(fit2)[[11]][11:20], col="#56B4E9", lty=2) ## lower
lines(1:10,summary(fit2)[[10]][21:30], col="#009E73", lty=2) ## upper
lines(1:10,summary(fit2)[[6]][21:30], col="#009E73", lwd=2) ## value sand 50
lines(1:10,summary(fit2)[[11]][21:30], col="#009E73", lty=2) ## lower
lines(1:10,summary(fit2)[[10]][31:40], col="#CC79A7", lty=2) ## upper
lines(1:10,summary(fit2)[[6]][31:40], col="#CC79A7", lwd=2) ## value sand 75
lines(1:10,summary(fit2)[[11]][31:40], col="#CC79A7", lty=2) ## lower
lines(1:10,summary(fit2)[[10]][41:50], col="#D55E00", lty=2) ## upper
lines(1:10,summary(fit2)[[6]][41:50], col="#D55E00", lwd=2) ## value sand 100
lines(1:10,summary(fit2)[[11]][41:50], col="#D55E00", lty=2) ## lower
legend(1.7, 0.44, c("0%","25%","50%","75%","100%"), lty=1, lwd=3, col=c("#E69F00","#56B4E9","#009E73","#CC79A7","#D55E00"), cex=1.2, title="Sand")

coxph.fit <- coxph(my.surv ~ Sand, method="breslow", data=substrate)
coxph.fit 

## raw number of germinants end trials

end <- subset(substrate, census==10)

## compare microsite

end.means <- end %>% group_by(Micro) %>% summarize(eph=mean(survival), eph.se=se(survival), Height=mean(height, na.rm=T), Height.se=se(height)) %>% gather(measure, value, 2:5) %>% separate(measure, c("Eph",".se")) ## calculate metrics and put long format
end.means[is.na(end.means$.se),3] <- "mean"
end.means <- end.means %>% spread(.se, value)
end.means <- data.frame(end.means)

end.means[,"lower"] <- end.means[,"mean"]-end.means[,"se"]
end.means[,"upper"] <- end.means[,"mean"]+end.means[,"se"]

survival <- subset(end.means, Eph=="eph")

plot1 <- ggplot(survival, aes(x=Micro, y=mean)) + geom_bar(stat="identity") +
  geom_errorbar(aes(ymin=lower, ymax=upper), width=.2)+ylab("average surviving Ephedra plant")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16)) + xlab("Microsite") 

height <- subset(end.means, Eph=="Height")

plot2 <- ggplot(height, aes(x=Micro, y=mean)) + geom_bar(stat="identity") +
  geom_errorbar(aes(ymin=lower, ymax=upper), width=.2)+ylab("average height of Ephedra plant")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16)) + xlab("Microsite") 

require(gridExtra)

grid.arrange(plot1, plot2, ncol=2)
m1 <- glm(survival~ Sand* Micro, data=end, family="binomial")
anova(m1, test="Chisq")

lsmeans(m1, pairwise~Sand)


## survival
end.means <- end %>% group_by(Sand) %>% summarize(eph=mean(survival), eph.se=se(survival))
end.means <- data.frame(end.means)

end.means[,"lower"] <- end.means[,"eph"]-end.means[,"eph.se"]
end.means[,"upper"] <- end.means[,"eph"]+end.means[,"eph.se"]

ggplot(end.means, aes(x=Sand, y=eph)) + geom_bar(stat="identity", fill="#56B4E9") +
  geom_errorbar(aes(ymin=lower, ymax=upper), width=.2)+ylab("average surviving Ephedra plant")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16)) + xlab("Percentage of sand in soil") 


## height

end.means <- end %>% group_by(Sand) %>% summarize(eph=mean(height, na.rm=T), eph.se=se(height, na.rm=T))
end.means <- data.frame(end.means)

end.means[,"lower"] <- end.means[,"eph"]-end.means[,"eph.se"]
end.means[,"upper"] <- end.means[,"eph"]+end.means[,"eph.se"]

ggplot(end.means, aes(x=Sand, y=eph)) + geom_bar(stat="identity", fill="#56B4E9") +
  geom_errorbar(aes(ymin=lower, ymax=upper), width=.2)+ylab("average surviving Ephedra plant")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16)) + xlab("Percentage of sand in soil") 


## most germinants
maximum.germ <- substrate %>% group_by(Micro, Sand, Rep) %>% summarize(eph.max=max(survival))

max.eph <- maximum.germ %>% group_by(Sand) %>% summarize(eph=mean(eph.max,na.rm=T),eph.se=se(eph.max, na.rm=T)) 
max.eph <- data.frame(max.eph)

max.eph[,"lower"] <- max.eph[,"eph"]-max.eph[,"eph.se"]
max.eph[,"upper"] <- max.eph[,"eph"]+max.eph[,"eph.se"]


ggplot(max.eph, aes(x=Sand, y=eph)) + geom_point(fill="black", size=4) +
  geom_errorbar(aes(ymin=lower, ymax=upper), width=.2)+ylab(expression("Average emerged plants of   "*italic("E. californica")))+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16)) + xlab("Percentage of sand in soil") + ylim(0,1) + stat_smooth(method="lm", formula= y~poly(x,2),data=max.eph, aes(x=as.numeric(Sand), y=eph), lwd=1, color="black", lty=2)

m1 <- lm(eph~poly(as.numeric(Sand),2), data=max.eph)
summary(m1)


## Difference between emergence and survival
substrate2 <- subset(substrate, census==10)
substrate2[,"diff"] <- subset(substrate, census==1, "survival")+subset(substrate, census==10,"survival")
substrate2 <- subset(substrate2, diff!=0) ## remove plots that had no plants
substrate2[,"diff"] <- substrate2[,"diff"]-1 ## binomial whether or not survived 


m2 <- glm(diff ~ Micro, family=binomial, data=substrate2)
anova(m2, test="Chisq")

Test of limiting factors - brome

recruit[is.na(recruit)] <- 0

## water
water <- subset(recruit, Treatment == "control" | Treatment=="water")

## germination
water.germ <- water %>% group_by(Density, Lvl) %>% summarize(eph=mean(ephedra.end ),brome=mean(brome.begin))

ggplot(water.germ) + geom_jitter(aes(x=Density, y=brome, fill=Lvl, color=Lvl), size=2)+ylab("number of Bromus germinants")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16))

m1 <- glm(brome.begin~Density *Lvl, data=water, family=poisson)
anova(m1, test="Chisq")
## Analysis of Deviance Table
## 
## Model: poisson, link: log
## 
## Response: brome.begin
## 
## Terms added sequentially (first to last)
## 
## 
##             Df Deviance Resid. Df Resid. Dev Pr(>Chi)    
## NULL                          299    1275.05             
## Density      1   849.52       298     425.53   <2e-16 ***
## Lvl          2     4.50       296     421.03   0.1053    
## Density:Lvl  2     0.00       294     421.03   0.9985    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## biomass
water.bio <- water %>% group_by(Density, Lvl) %>% summarize(eph=mean(Ephedra.biomass ),brome=mean(brome.biomass))

ggplot(water.bio) + geom_jitter(aes(x=Density, y=brome, fill=Lvl, color=Lvl), size=2)+ylab("final biomass of Brome")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16))

## clipping
clip <- subset(recruit, Treatment == "control" | Treatment=="clipped")

## germination
clip.germ <- clip %>% group_by(Density, Lvl) %>% summarize(eph=mean(ephedra.end ),brome=mean(brome.begin))

ggplot(clip.germ) + geom_jitter(aes(x=Density, y=brome, fill=Lvl, color=Lvl), size=2)+ylab("number of Bromus germinants")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16))

## biomass
clip.bio <- clip %>% group_by(Density, Lvl) %>% summarize(eph=mean(Ephedra.biomass ),brome=mean(brome.biomass))

ggplot(clip.bio) + geom_jitter(aes(x=Density, y=brome, fill=Lvl, color=Lvl), size=2)+ylab("final biomass of Brome")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16))

m1 <- glm(brome.begin~Density *Lvl, data=clip, family=poisson)
anova(m1, test="Chisq")
## Analysis of Deviance Table
## 
## Model: poisson, link: log
## 
## Response: brome.begin
## 
## Terms added sequentially (first to last)
## 
## 
##             Df Deviance Resid. Df Resid. Dev Pr(>Chi)    
## NULL                          299    1332.93             
## Density      1   863.30       298     469.63   <2e-16 ***
## Lvl          2     3.66       296     465.97   0.1605    
## Density:Lvl  2     0.04       294     465.93   0.9814    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## shade
shade <- subset(recruit, Treatment == "control" | Treatment=="shade")

## germination
shade.germ <- shade %>% group_by(Density, Lvl) %>% summarize(eph=mean(ephedra.end ),brome=mean(brome.begin))

ggplot(shade.germ) + geom_jitter(aes(x=Density, y=brome, fill=Lvl, color=Lvl), size=2)+ylab("number of Bromus germinants")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16))

## biomass
shade.bio <- shade %>% group_by(Density, Lvl) %>% summarize(eph=mean(Ephedra.biomass ),brome=mean(brome.biomass))

ggplot(shade.bio) + geom_jitter(aes(x=Density, y=brome, fill=Lvl, color=Lvl), size=2)+ylab("final biomass of Brome")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16))

m1 <- glm(brome.begin~Density *Lvl, data=shade, family=poisson)
anova(m1, test="Chisq")
## Analysis of Deviance Table
## 
## Model: poisson, link: log
## 
## Response: brome.begin
## 
## Terms added sequentially (first to last)
## 
## 
##             Df Deviance Resid. Df Resid. Dev  Pr(>Chi)    
## NULL                          299    1221.52              
## Density      1   804.97       298     416.55 < 2.2e-16 ***
## Lvl          2    13.34       296     403.21  0.001267 ** 
## Density:Lvl  2     0.22       294     402.98  0.894507    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Test of limiting factors - Ephedra

## water
## germination

ggplot(water.germ) + geom_jitter(aes(x=Density, y=eph, fill=Lvl, color=Lvl), size=2)+ylab("number of Ephedra germinants")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16))

## biomass

ggplot(water.bio) + geom_jitter(aes(x=Density, y=eph, fill=Lvl, color=Lvl), size=2)+ylab("final biomass of Ephedra")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16))

## clipping

## germination

ggplot(clip.germ) + geom_jitter(aes(x=Density, y=eph, fill=Lvl, color=Lvl), size=2)+ylab("number of Ephedra germinants")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16))

## biomass

ggplot(clip.bio) + geom_jitter(aes(x=Density, y=eph, fill=Lvl, color=Lvl), size=2)+ylab("final biomass of Ephedra")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16))

m1 <- glm(ephedra.end~Density *Lvl, data=clip, family=poisson)
anova(m1, test="Chisq")
## Analysis of Deviance Table
## 
## Model: poisson, link: log
## 
## Response: ephedra.end
## 
## Terms added sequentially (first to last)
## 
## 
##             Df Deviance Resid. Df Resid. Dev Pr(>Chi)  
## NULL                          299     220.71           
## Density      1  2.73641       298     217.97  0.09808 .
## Lvl          2  0.34733       296     217.63  0.84058  
## Density:Lvl  2  0.47792       294     217.15  0.78745  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## shade

## germination

ggplot(shade.germ) + geom_jitter(aes(x=Density, y=eph, fill=Lvl, color=Lvl), size=2)+ylab("number of Ephedra germinants")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16))

##biomass
ggplot(shade.bio) + geom_jitter(aes(x=Density, y=eph, fill=Lvl, color=Lvl), size=2)+ylab("final biomass of Ephedra")+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),panel.background = element_blank(),axis.text=element_text(size=14),axis.title=element_text(size=16))

m1 <- glm(brome.begin~Density *Lvl, data=shade, family=poisson)
anova(m1, test="Chisq")
## Analysis of Deviance Table
## 
## Model: poisson, link: log
## 
## Response: brome.begin
## 
## Terms added sequentially (first to last)
## 
## 
##             Df Deviance Resid. Df Resid. Dev  Pr(>Chi)    
## NULL                          299    1221.52              
## Density      1   804.97       298     416.55 < 2.2e-16 ***
## Lvl          2    13.34       296     403.21  0.001267 ** 
## Density:Lvl  2     0.22       294     402.98  0.894507    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Summarized GLMs for manuscript

## Water
m1 <- glm(ephedra.end~ Density *Lvl , data=water, family=binomial)
anova(m1, test="Chisq")
## Analysis of Deviance Table
## 
## Model: binomial, link: logit
## 
## Response: ephedra.end
## 
## Terms added sequentially (first to last)
## 
## 
##             Df Deviance Resid. Df Resid. Dev Pr(>Chi)  
## NULL                          299     397.45           
## Density      1  2.78375       298     394.66  0.09522 .
## Lvl          2  0.20096       296     394.46  0.90440  
## Density:Lvl  2  0.08676       294     394.37  0.95755  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
m1.bio <- glm(Ephedra.biomass~Density *Lvl, data=subset(water, Ephedra.biomass>0, family=Gamma))
anova(m1.bio, test="Chisq")
## Analysis of Deviance Table
## 
## Model: gaussian, link: identity
## 
## Response: Ephedra.biomass
## 
## Terms added sequentially (first to last)
## 
## 
##             Df   Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL                            106   0.057926         
## Density      1 0.00022241       105   0.057704   0.5282
## Lvl          2 0.00019973       103   0.057504   0.8364
## Density:Lvl  2 0.00103890       101   0.056465   0.3949
## Shade
m2 <- glm(ephedra.end~ Density *Lvl, data=shade, family=binomial)
anova(m2, test="Chisq")
## Analysis of Deviance Table
## 
## Model: binomial, link: logit
## 
## Response: ephedra.end
## 
## Terms added sequentially (first to last)
## 
## 
##             Df Deviance Resid. Df Resid. Dev Pr(>Chi)   
## NULL                          299     368.20            
## Density      1   0.7330       298     367.46 0.391927   
## Lvl          2  11.4709       296     355.99 0.003229 **
## Density:Lvl  2   1.4327       294     354.56 0.488533   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
m2.bio <- glm(Ephedra.biomass~Density *Lvl , data=subset(shade, Ephedra.biomass>0), family=Gamma)
anova(m2.bio, test="Chisq")
## Analysis of Deviance Table
## 
## Model: Gamma, link: inverse
## 
## Response: Ephedra.biomass
## 
## Terms added sequentially (first to last)
## 
## 
##             Df Deviance Resid. Df Resid. Dev Pr(>Chi)  
## NULL                           67     25.637           
## Density      1  0.39889        66     25.238  0.23231  
## Lvl          2  2.02160        64     23.217  0.02691 *
## Density:Lvl  2  0.02846        62     23.188  0.95038  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Clipping
m3 <- glm(ephedra.end~ Density *Lvl, data=clip, family=binomial)
anova(m3, test="Chisq")
## Analysis of Deviance Table
## 
## Model: binomial, link: logit
## 
## Response: ephedra.end
## 
## Terms added sequentially (first to last)
## 
## 
##             Df Deviance Resid. Df Resid. Dev Pr(>Chi)  
## NULL                          299     393.19           
## Density      1   4.2054       298     388.98   0.0403 *
## Lvl          2   0.5545       296     388.43   0.7579  
## Density:Lvl  2   0.8190       294     387.61   0.6640  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
m3.bio <- glm(Ephedra.biomass~Density *Lvl, data=subset(clip, Ephedra.biomass>0), family=Gamma)
anova(m3.bio, test="Chisq")
## Analysis of Deviance Table
## 
## Model: Gamma, link: inverse
## 
## Response: Ephedra.biomass
## 
## Terms added sequentially (first to last)
## 
## 
##             Df Deviance Resid. Df Resid. Dev Pr(>Chi)    
## NULL                          106     48.613             
## Density      1   0.6174       105     47.996   0.1774    
## Lvl          2   9.2947       103     38.701 1.13e-06 ***
## Density:Lvl  2   0.9905       101     37.711   0.2324    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
m4 <-  glm(ephedra.end~brome.begin, data=recruit, family=binomial)
anova(m4, test="Chisq")
## Analysis of Deviance Table
## 
## Model: binomial, link: logit
## 
## Response: ephedra.end
## 
## Terms added sequentially (first to last)
## 
## 
##             Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL                          699     901.37         
## brome.begin  1   2.0214       698     899.35   0.1551
m4.bio <-  glm(Ephedra.biomass~brome.begin, data=subset(recruit, Ephedra.biomass>0 ), family=Gamma)
anova(m4.bio, test="Chisq")
## Analysis of Deviance Table
## 
## Model: Gamma, link: inverse
## 
## Response: Ephedra.biomass
## 
## Terms added sequentially (first to last)
## 
## 
##             Df  Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL                           209     89.330         
## brome.begin  1 0.0012905       208     89.328    0.953
## brome comparisons
library(lme4)
## Loading required package: Matrix
## 
## Attaching package: 'Matrix'
## The following objects are masked from 'package:tidyr':
## 
##     expand, pack, unpack
## Water
m1 <- glm(brome.begin/Density~ Lvl, weights=Density, data=subset(water, Density>0), family=binomial)
anova(m1, test="Chisq")
## Analysis of Deviance Table
## 
## Model: binomial, link: logit
## 
## Response: brome.begin/Density
## 
## Terms added sequentially (first to last)
## 
## 
##      Df Deviance Resid. Df Resid. Dev Pr(>Chi)   
## NULL                   239     475.39            
## Lvl   2   10.831       237     464.56 0.004447 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Shade
m2 <- glm(brome.begin/Density~ Lvl, weights=Density, data=subset(shade, Density>0), family=binomial)
anova(m2, test="Chisq")
## Analysis of Deviance Table
## 
## Model: binomial, link: logit
## 
## Response: brome.begin/Density
## 
## Terms added sequentially (first to last)
## 
## 
##      Df Deviance Resid. Df Resid. Dev  Pr(>Chi)    
## NULL                   239     429.07              
## Lvl   2   31.496       237     397.57 1.448e-07 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Clipping
m3<- glm(brome.begin/Density~ Lvl, weights=Density, data=subset(clip, Density>0), family=binomial)
anova(m3, test="Chisq")
## Analysis of Deviance Table
## 
## Model: binomial, link: logit
## 
## Response: brome.begin/Density
## 
## Terms added sequentially (first to last)
## 
## 
##      Df Deviance Resid. Df Resid. Dev Pr(>Chi)  
## NULL                   239     528.32           
## Lvl   2    8.962       237     519.35  0.01132 *
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Brome density vs Ephedra

dense <- recruit %>% filter(Ephedra.biomass>0) %>%  group_by(brome.begin) %>% summarize(bio=mean(Ephedra.biomass), recruit=mean(ephedra.end), germ=mean(ephedra.begin), abv.grd=mean(Ephedra.above),blw.grd=mean(Ephedra.below))

ggplot(dense, aes(x=brome.begin, y=bio))+geom_point()+ theme_Publication() +ylab("E. californica biomass") + xlab("brome density") + geom_smooth(method=lm, formula= y ~ poly(x,2))
## Warning: `legend.margin` must be specified using `margin()`. For the old
## behavior use legend.spacing
## Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family not
## found in Windows font database

## Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family not
## found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

m1 <- lm(bio~poly(brome.begin,2), data=dense)

## recruitment no effect
ggplot(dense, aes(x=brome.begin, y=recruit))+geom_point()+ theme_Publication() +ylab("E. californica biomass") + xlab("brome density") #+ geom_smooth(method=lm, formula= y ~ x)
## Warning: `legend.margin` must be specified using `margin()`. For the old
## behavior use legend.spacing
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

m2 <- lm(recruit~brome.begin, data=dense)

## germination no effect
ggplot(dense, aes(x=brome.begin, y=germ))+geom_point()+ theme_Publication() +ylab("E. californica biomass") + xlab("brome density") #+ geom_smooth(method=lm, formula= y ~ x)
## Warning: `legend.margin` must be specified using `margin()`. For the old
## behavior use legend.spacing
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

m3 <- lm(germ~brome.begin, data=dense)


## above ground biomass 
ggplot(dense, aes(x=brome.begin, y=abv.grd))+geom_point()+ theme_Publication() +ylab("above-ground biomass") + xlab(expression(italic("B. madritensis")*" density")) + geom_smooth(method=lm, formula= y ~ x)+ xlim(0,20)
## Warning: `legend.margin` must be specified using `margin()`. For the old
## behavior use legend.spacing
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

m4 <- lm(abv.grd~brome.begin, data=dense)
summary(m4)
## 
## Call:
## lm(formula = abv.grd ~ brome.begin, data = dense)
## 
## Residuals:
##       Min        1Q    Median        3Q       Max 
## -0.011652 -0.004168 -0.001584  0.002695  0.014099 
## 
## Coefficients:
##               Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  0.0340643  0.0034082   9.995  9.4e-08 ***
## brome.begin -0.0007295  0.0003824  -1.908   0.0772 .  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.007214 on 14 degrees of freedom
## Multiple R-squared:  0.2063, Adjusted R-squared:  0.1496 
## F-statistic: 3.639 on 1 and 14 DF,  p-value: 0.07717
## below ground biomass
ggplot(dense, aes(x=brome.begin, y=blw.grd))+geom_point()+ theme_Publication() +ylab("below-ground biomass") + xlab(expression(italic("B. madritensis")*" density")) + geom_smooth(method=lm, formula= y ~ poly(x,2)) + xlim(0,20)
## Warning: `legend.margin` must be specified using `margin()`. For the old
## behavior use legend.spacing
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

m5 <- lm(blw.grd~poly(brome.begin,2), data=dense)
summary(m5)
## 
## Call:
## lm(formula = blw.grd ~ poly(brome.begin, 2), data = dense)
## 
## Residuals:
##        Min         1Q     Median         3Q        Max 
## -0.0014710 -0.0007298 -0.0001058  0.0005620  0.0015789 
## 
## Coefficients:
##                         Estimate Std. Error t value Pr(>|t|)    
## (Intercept)            0.0049697  0.0002432   20.44 2.89e-11 ***
## poly(brome.begin, 2)1 -0.0036473  0.0009726   -3.75  0.00243 ** 
## poly(brome.begin, 2)2 -0.0032968  0.0009726   -3.39  0.00484 ** 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.0009726 on 13 degrees of freedom
## Multiple R-squared:  0.6628, Adjusted R-squared:  0.6109 
## F-statistic: 12.78 on 2 and 13 DF,  p-value: 0.0008538

Compare regression co-efficients

library(broom)
recruit[is.na(recruit)] <- 0

## unique test
recruit[,"test"] <- paste0(recruit$Treatment,"-", recruit$Lvl)
biomass <- recruit %>% filter(Ephedra.biomass  > 0)

## join above and below
biolong <- biomass %>% gather(biomass, value, 14:15)

## conduct linear regression against brome density
regdata <- biolong %>% group_by(test, biomass) %>%
  do(lmOut = lm(log(value+0.0001) ~ poly(Density,2), data = .))
regcoef <- tidy(regdata, lmOut) %>% data.frame(.)  %>%  filter(term != "(Intercept)")
regcoef
##             test       biomass              term    estimate std.error
## 1   clipped-once Ephedra.above poly(Density, 2)1  0.27481615 0.6500371
## 2   clipped-once Ephedra.above poly(Density, 2)2 -0.14744877 0.6500371
## 3   clipped-once Ephedra.below poly(Density, 2)1  0.04790895 0.6388036
## 4   clipped-once Ephedra.below poly(Density, 2)2 -0.28040085 0.6388036
## 5  clipped-twice Ephedra.above poly(Density, 2)1 -0.78009563 0.6431364
## 6  clipped-twice Ephedra.above poly(Density, 2)2  1.07444554 0.6431364
## 7  clipped-twice Ephedra.below poly(Density, 2)1 -1.92114529 1.0557950
## 8  clipped-twice Ephedra.below poly(Density, 2)2 -1.12703841 1.0557950
## 9   control-none Ephedra.above poly(Density, 2)1 -2.41688646 1.0951954
## 10  control-none Ephedra.above poly(Density, 2)2 -1.63307394 1.0951954
## 11  control-none Ephedra.below poly(Density, 2)1 -0.87529650 1.1265107
## 12  control-none Ephedra.below poly(Density, 2)2 -1.45749959 1.1265107
## 13    shade-high Ephedra.above poly(Density, 2)1 -0.31628449 0.5460872
## 14    shade-high Ephedra.above poly(Density, 2)2 -0.34996609 0.5460872
## 15    shade-high Ephedra.below poly(Density, 2)1  0.04497215 0.7463155
## 16    shade-high Ephedra.below poly(Density, 2)2 -0.63676727 0.7463155
## 17     shade-med Ephedra.above poly(Density, 2)1 -0.43816008 0.7630626
## 18     shade-med Ephedra.above poly(Density, 2)2  0.07223617 0.7630626
## 19     shade-med Ephedra.below poly(Density, 2)1  0.69814968 0.7879161
## 20     shade-med Ephedra.below poly(Density, 2)2  0.09286347 0.7879161
## 21    water-high Ephedra.above poly(Density, 2)1  0.70269145 0.7806290
## 22    water-high Ephedra.above poly(Density, 2)2  0.25087933 0.7806290
## 23    water-high Ephedra.below poly(Density, 2)1 -0.22801320 1.1941965
## 24    water-high Ephedra.below poly(Density, 2)2 -1.11860350 1.1941965
## 25     water-low Ephedra.above poly(Density, 2)1  0.59110674 0.6219097
## 26     water-low Ephedra.above poly(Density, 2)2 -0.02386899 0.6219097
## 27     water-low Ephedra.below poly(Density, 2)1 -1.26964812 1.1063110
## 28     water-low Ephedra.below poly(Density, 2)2 -1.08669728 1.1063110
##      statistic    p.value
## 1   0.42276995 0.67558161
## 2  -0.22683131 0.82214630
## 3   0.07499793 0.94073133
## 4  -0.43894689 0.66395317
## 5  -1.21295525 0.23304633
## 6   1.67063411 0.10346703
## 7  -1.81961969 0.07714106
## 8  -1.06747850 0.29286225
## 9  -2.20680834 0.03439420
## 10 -1.49112557 0.14542654
## 11 -0.77699792 0.44269442
## 12 -1.29381775 0.20471093
## 13 -0.57918309 0.57106186
## 14 -0.64086116 0.53128268
## 15  0.06025890 0.95274496
## 16 -0.85321458 0.40695901
## 17 -0.57421247 0.57737725
## 18  0.09466611 0.92628248
## 19  0.88607106 0.39453765
## 20  0.11785958 0.90830350
## 21  0.90016063 0.37418692
## 22  0.32138102 0.74983309
## 23 -0.19093441 0.84968025
## 24 -0.93669973 0.35533185
## 25  0.95047037 0.34946828
## 26 -0.03838015 0.96963886
## 27 -1.14764120 0.26018664
## 28 -0.98227104 0.33382220
## compare root vs shoot linear-models only
regdata <- biolong %>% group_by(test, biomass) %>%
  do(lmOut = lm(log(value+0.0001) ~ Density -1, data = .))
regcoef <- tidy(regdata, lmOut) %>% data.frame(.)  %>%  filter(term != "(Intercept)")
regcoef
##             test       biomass    term   estimate  std.error statistic
## 1   clipped-once Ephedra.above Density -0.2626104 0.04651326 -5.645926
## 2   clipped-once Ephedra.below Density -0.3696163 0.06326839 -5.842037
## 3  clipped-twice Ephedra.above Density -0.2941285 0.05045686 -5.829307
## 4  clipped-twice Ephedra.below Density -0.4189320 0.06924742 -6.049785
## 5   control-none Ephedra.above Density -0.3283941 0.05086589 -6.456077
## 6   control-none Ephedra.below Density -0.4483319 0.07767200 -5.772117
## 7     shade-high Ephedra.above Density -0.2433404 0.05849616 -4.159938
## 8     shade-high Ephedra.below Density -0.3750912 0.09368469 -4.003762
## 9      shade-med Ephedra.above Density -0.2579739 0.05442674 -4.739838
## 10     shade-med Ephedra.below Density -0.3667645 0.08642932 -4.243520
## 11    water-high Ephedra.above Density -0.2273466 0.04499472 -5.052740
## 12    water-high Ephedra.below Density -0.3611560 0.06632018 -5.445642
## 13     water-low Ephedra.above Density -0.2492054 0.04295041 -5.802165
## 14     water-low Ephedra.below Density -0.4236047 0.06414468 -6.603895
##         p.value
## 1  3.371231e-06
## 2  1.924762e-06
## 3  9.761705e-07
## 4  4.864409e-07
## 5  1.945196e-07
## 6  1.541832e-06
## 7  6.559799e-04
## 8  9.196789e-04
## 9  3.864364e-04
## 10 9.586756e-04
## 11 1.198334e-05
## 12 3.536915e-06
## 13 1.926020e-06
## 14 1.912173e-07
## Test above vs below response to brome on density gradient
t.test(estimate ~ biomass, data=regcoef)
## 
##  Welch Two Sample t-test
## 
## data:  estimate by biomass
## t = 6.9796, df = 11.998, p-value = 1.477e-05
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  0.08848354 0.16880138
## sample estimates:
## mean in group Ephedra.above mean in group Ephedra.below 
##                  -0.2661428                  -0.3947852
## Check against brome Biomass
regdata <- biolong %>% group_by(test, biomass) %>%
  do(lmOut = lm(log(value+0.0001) ~ brome.biomass -1 , data = .))
biolong %>% group_by(test, biomass) %>% summarize(n=length(value))
## # A tibble: 14 x 3
## # Groups:   test [7]
##    test          biomass           n
##    <chr>         <chr>         <int>
##  1 clipped-once  Ephedra.above    32
##  2 clipped-once  Ephedra.below    32
##  3 clipped-twice Ephedra.above    39
##  4 clipped-twice Ephedra.below    39
##  5 control-none  Ephedra.above    36
##  6 control-none  Ephedra.below    36
##  7 shade-high    Ephedra.above    18
##  8 shade-high    Ephedra.below    18
##  9 shade-med     Ephedra.above    14
## 10 shade-med     Ephedra.below    14
## 11 water-high    Ephedra.above    38
## 12 water-high    Ephedra.below    38
## 13 water-low     Ephedra.above    33
## 14 water-low     Ephedra.below    33
regcoef <- tidy(regdata, lmOut, n) %>% data.frame(.)  %>%  filter(term != "(Intercept)")
regcoef
##             test       biomass          term   estimate std.error statistic
## 1   clipped-once Ephedra.above brome.biomass -13.385395 1.6020711 -8.355057
## 2   clipped-once Ephedra.below brome.biomass -18.346804 2.2665821 -8.094480
## 3  clipped-twice Ephedra.above brome.biomass -18.029511 3.1979346 -5.637861
## 4  clipped-twice Ephedra.below brome.biomass -25.726637 4.3868000 -5.864557
## 5   control-none Ephedra.above brome.biomass  -8.229579 1.4216487 -5.788757
## 6   control-none Ephedra.below brome.biomass -12.784337 1.8838040 -6.786447
## 7     shade-high Ephedra.above brome.biomass  -9.344363 3.0416655 -3.072120
## 8     shade-high Ephedra.below brome.biomass -14.371476 4.8356921 -2.971958
## 9      shade-med Ephedra.above brome.biomass -11.845188 2.6007340 -4.554556
## 10     shade-med Ephedra.below brome.biomass -16.181929 4.3086956 -3.755645
## 11    water-high Ephedra.above brome.biomass  -1.636745 0.3202788 -5.110377
## 12    water-high Ephedra.below brome.biomass  -2.517458 0.4836808 -5.204793
## 13     water-low Ephedra.above brome.biomass  -3.151942 0.6876007 -4.583972
## 14     water-low Ephedra.below brome.biomass  -5.063517 1.1001728 -4.602474
##         p.value
## 1  1.944844e-09
## 2  3.848959e-09
## 3  1.787076e-06
## 4  8.732890e-07
## 5  1.465849e-06
## 6  7.219249e-08
## 7  6.904691e-03
## 8  8.550531e-03
## 9  5.406319e-04
## 10 2.401544e-03
## 11 1.002474e-05
## 12 7.480114e-06
## 13 6.629695e-05
## 14 6.285306e-05
## Test root vs shoot
t.test(estimate ~ biomass, data=regcoef)
## 
##  Welch Two Sample t-test
## 
## data:  estimate by biomass
## t = 1.1387, df = 10.954, p-value = 0.2791
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -3.918299 12.309566
## sample estimates:
## mean in group Ephedra.above mean in group Ephedra.below 
##                   -9.374675                  -13.570308
## rename test column
newframe <- data.frame(test=unique(regcoef$test), treatments=c("clip-1", "clip-2","control","high shade","med shade","high water","low water"), sorting=c(2,3,1,5,4,7,6))  
newframe <- rbind(newframe, newframe)                   
newframe[,"biomass"]  <- rep(unique(regcoef$biomass), each=7) 
newframe[,"tissue"] <- rep(c("aboveground","belowground"), each=7)


coefplot <- merge(regcoef, newframe, by=c("test","biomass"))
coefplot[order(coefplot$sorting),]
##             test       biomass          term   estimate std.error statistic
## 5   control-none Ephedra.above brome.biomass  -8.229579 1.4216487 -5.788757
## 6   control-none Ephedra.below brome.biomass -12.784337 1.8838040 -6.786447
## 1   clipped-once Ephedra.above brome.biomass -13.385395 1.6020711 -8.355057
## 2   clipped-once Ephedra.below brome.biomass -18.346804 2.2665821 -8.094480
## 3  clipped-twice Ephedra.above brome.biomass -18.029511 3.1979346 -5.637861
## 4  clipped-twice Ephedra.below brome.biomass -25.726637 4.3868000 -5.864557
## 9      shade-med Ephedra.above brome.biomass -11.845188 2.6007340 -4.554556
## 10     shade-med Ephedra.below brome.biomass -16.181929 4.3086956 -3.755645
## 7     shade-high Ephedra.above brome.biomass  -9.344363 3.0416655 -3.072120
## 8     shade-high Ephedra.below brome.biomass -14.371476 4.8356921 -2.971958
## 13     water-low Ephedra.above brome.biomass  -3.151942 0.6876007 -4.583972
## 14     water-low Ephedra.below brome.biomass  -5.063517 1.1001728 -4.602474
## 11    water-high Ephedra.above brome.biomass  -1.636745 0.3202788 -5.110377
## 12    water-high Ephedra.below brome.biomass  -2.517458 0.4836808 -5.204793
##         p.value treatments sorting      tissue
## 5  1.465849e-06    control       1 aboveground
## 6  7.219249e-08    control       1 belowground
## 1  1.944844e-09     clip-1       2 aboveground
## 2  3.848959e-09     clip-1       2 belowground
## 3  1.787076e-06     clip-2       3 aboveground
## 4  8.732890e-07     clip-2       3 belowground
## 9  5.406319e-04  med shade       4 aboveground
## 10 2.401544e-03  med shade       4 belowground
## 7  6.904691e-03 high shade       5 aboveground
## 8  8.550531e-03 high shade       5 belowground
## 13 6.629695e-05  low water       6 aboveground
## 14 6.285306e-05  low water       6 belowground
## 11 1.002474e-05 high water       7 aboveground
## 12 7.480114e-06 high water       7 belowground
coefplot$treatments <- reorder(coefplot$treatments, coefplot$sorting)

## plot regression coefficients
ggplot(coefplot, aes(x=treatments, y=estimate)) + geom_point(size=3) + facet_grid(~tissue) + theme_Publication() + geom_errorbar(aes(x=treatments, ymin=estimate-std.error, ymax=estimate+std.error), width=0) + xlab("") + ylab("B. madritnesis effect")
## Warning: `legend.margin` must be specified using `margin()`. For the old
## behavior use legend.spacing
## Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family not
## found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## plot raw biomass among treatments
bioavg <- biolong %>% group_by(test, biomass) %>% summarize(bio=mean(value), error=se(value))
bioavg <- merge(bioavg, newframe)

bioavg$treatments <- reorder(bioavg$treatments, bioavg$sorting)

ggplot(bioavg, aes(x=treatments, y=bio, fill=tissue)) + geom_bar(stat="identity", position=position_dodge(width=0.9), color="black") + ylab("biomass (g)") + theme_Publication() + geom_errorbar(aes(x=treatments, ymin=bio-error, ymax=bio+error), position=position_dodge(width=0.9), width=0) + xlab("") + scale_fill_brewer()
## Warning: `legend.margin` must be specified using `margin()`. For the old
## behavior use legend.spacing
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

ANCOVA and probability of establishment

## unique test
recruit[,"test"] <- paste0(recruit$Treatment,"-", recruit$Lvl)
recruit[is.na(recruit)] <- 0
biomass <- recruit %>% filter(Ephedra.biomass  > 0 & Ephedra.biomass < 0.6)


library(emmeans)


## Compare Emergence
m1 <- glm(ephedra.begin ~ Density* test, data=recruit, family="binomial")
anova(m1, test="Chisq")
## Analysis of Deviance Table
## 
## Model: binomial, link: logit
## 
## Response: ephedra.begin
## 
## Terms added sequentially (first to last)
## 
## 
##              Df Deviance Resid. Df Resid. Dev  Pr(>Chi)    
## NULL                           699     965.59              
## Density       1   3.5657       698     962.03   0.05898 .  
## test          6  30.5072       692     931.52 3.147e-05 ***
## Density:test  6   6.4480       686     925.07   0.37492    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
emmeans(m1, pairwise~test, var="ephedra.begin")
## NOTE: Results may be misleading due to involvement in interactions
## $emmeans
##  test          emmean    SE  df asymp.LCL asymp.UCL
##  clipped-once  -0.120 0.201 Inf   -0.5135    0.2727
##  clipped-twice -0.286 0.203 Inf   -0.6849    0.1125
##  control-none   0.201 0.201 Inf   -0.1933    0.5951
##  shade-high    -0.490 0.206 Inf   -0.8936   -0.0858
##  shade-med     -1.061 0.249 Inf   -1.5487   -0.5740
##  water-high     0.493 0.207 Inf    0.0876    0.8992
##  water-low     -0.080 0.200 Inf   -0.4723    0.3123
## 
## Results are given on the logit (not the response) scale. 
## Confidence level used: 0.95 
## 
## $contrasts
##  contrast                     estimate    SE  df z.ratio p.value
##  clipped-once - clipped-twice   0.1658 0.286 Inf  0.580  0.9974 
##  clipped-once - control-none   -0.3213 0.284 Inf -1.131  0.9186 
##  clipped-once - shade-high      0.3693 0.288 Inf  1.284  0.8595 
##  clipped-once - shade-med       0.9409 0.319 Inf  2.945  0.0504 
##  clipped-once - water-high     -0.6138 0.288 Inf -2.129  0.3352 
##  clipped-once - water-low      -0.0404 0.283 Inf -0.143  1.0000 
##  clipped-twice - control-none  -0.4871 0.286 Inf -1.703  0.6142 
##  clipped-twice - shade-high     0.2035 0.290 Inf  0.703  0.9925 
##  clipped-twice - shade-med      0.7751 0.321 Inf  2.413  0.1930 
##  clipped-twice - water-high    -0.7796 0.290 Inf -2.686  0.1017 
##  clipped-twice - water-low     -0.2062 0.285 Inf -0.723  0.9913 
##  control-none - shade-high      0.6906 0.288 Inf  2.398  0.1991 
##  control-none - shade-med       1.2623 0.320 Inf  3.947  0.0015 
##  control-none - water-high     -0.2925 0.289 Inf -1.013  0.9512 
##  control-none - water-low       0.2809 0.284 Inf  0.990  0.9563 
##  shade-high - shade-med         0.5717 0.323 Inf  1.770  0.5683 
##  shade-high - water-high       -0.9831 0.292 Inf -3.365  0.0135 
##  shade-high - water-low        -0.4096 0.287 Inf -1.426  0.7879 
##  shade-med - water-high        -1.5547 0.324 Inf -4.805  <.0001 
##  shade-med - water-low         -0.9813 0.319 Inf -3.074  0.0344 
##  water-high - water-low         0.5734 0.288 Inf  1.991  0.4202 
## 
## Results are given on the log odds ratio (not the response) scale. 
## P value adjustment: tukey method for comparing a family of 7 estimates
## Compare Establishment
m2 <- glm(ephedra.end ~ Density* test, data=recruit, family="binomial")
anova(m2, test="Chisq")
## Analysis of Deviance Table
## 
## Model: binomial, link: logit
## 
## Response: ephedra.end
## 
## Terms added sequentially (first to last)
## 
## 
##              Df Deviance Resid. Df Resid. Dev Pr(>Chi)  
## NULL                           699     901.37           
## Density       1   4.9171       698     896.46  0.02659 *
## test          6  16.2032       692     880.25  0.01270 *
## Density:test  6   2.9002       686     877.35  0.82127  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
emmeans(m2, pairwise~test, var="ephedra.end")
## NOTE: Results may be misleading due to involvement in interactions
## $emmeans
##  test          emmean    SE  df asymp.LCL asymp.UCL
##  clipped-once  -0.666 0.212 Inf    -1.081   -0.2512
##  clipped-twice -0.469 0.210 Inf    -0.881   -0.0568
##  control-none  -0.583 0.210 Inf    -0.994   -0.1712
##  shade-high    -0.533 0.207 Inf    -0.939   -0.1267
##  shade-med     -1.539 0.266 Inf    -2.060   -1.0182
##  water-high    -0.454 0.207 Inf    -0.859   -0.0489
##  water-low     -0.493 0.207 Inf    -0.898   -0.0873
## 
## Results are given on the logit (not the response) scale. 
## Confidence level used: 0.95 
## 
## $contrasts
##  contrast                     estimate    SE  df z.ratio p.value
##  clipped-once - clipped-twice  -0.1974 0.298 Inf -0.662  0.9946 
##  clipped-once - control-none   -0.0833 0.298 Inf -0.279  1.0000 
##  clipped-once - shade-high     -0.1331 0.296 Inf -0.449  0.9994 
##  clipped-once - shade-med       0.8730 0.340 Inf  2.569  0.1354 
##  clipped-once - water-high     -0.2121 0.296 Inf -0.717  0.9916 
##  clipped-once - water-low      -0.1736 0.296 Inf -0.587  0.9972 
##  clipped-twice - control-none   0.1141 0.297 Inf  0.384  0.9998 
##  clipped-twice - shade-high     0.0643 0.295 Inf  0.218  1.0000 
##  clipped-twice - shade-med      1.0704 0.339 Inf  3.159  0.0265 
##  clipped-twice - water-high    -0.0147 0.295 Inf -0.050  1.0000 
##  clipped-twice - water-low      0.0238 0.295 Inf  0.081  1.0000 
##  control-none - shade-high     -0.0498 0.295 Inf -0.169  1.0000 
##  control-none - shade-med       0.9563 0.339 Inf  2.823  0.0709 
##  control-none - water-high     -0.1288 0.295 Inf -0.437  0.9995 
##  control-none - water-low      -0.0903 0.295 Inf -0.306  0.9999 
##  shade-high - shade-med         1.0061 0.337 Inf  2.985  0.0449 
##  shade-high - water-high       -0.0790 0.293 Inf -0.270  1.0000 
##  shade-high - water-low        -0.0405 0.293 Inf -0.138  1.0000 
##  shade-med - water-high        -1.0851 0.337 Inf -3.223  0.0216 
##  shade-med - water-low         -1.0466 0.337 Inf -3.108  0.0310 
##  water-high - water-low         0.0385 0.292 Inf  0.132  1.0000 
## 
## Results are given on the log odds ratio (not the response) scale. 
## P value adjustment: tukey method for comparing a family of 7 estimates
## Compare growth
m3 <- lm(sqrt(Ephedra.above+0.001) ~ test * brome.biomass, data=biomass)
anova(m3)
## Analysis of Variance Table
## 
## Response: sqrt(Ephedra.above + 0.001)
##                     Df  Sum Sq   Mean Sq F value    Pr(>F)    
## test                 6 0.11764 0.0196070  8.1532 7.038e-08 ***
## brome.biomass        1 0.00040 0.0003956  0.1645   0.68547    
## test:brome.biomass   6 0.03015 0.0050243  2.0893   0.05613 .  
## Residuals          196 0.47134 0.0024048                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## compare pairwise comparisons
interact <- lstrends(m3,  ~ test , var = "brome.biomass")
contrast(interact,         list("clipped"=c(.5,.5,-1,0,0,0,0),"shade"=c(0,0,-1,.5,.5,0,0),"water"=c(0,0,-1,0,0,.5,.5)))
## Note: Use 'contrast(regrid(object), ...)' to obtain contrasts of back-transformed estimates
##  contrast estimate     SE  df t.ratio p.value
##  clipped   -0.0718 0.0607 196 -1.182  0.2386 
##  shade     -0.1604 0.0625 196 -2.568  0.0110 
##  water     -0.0639 0.0406 196 -1.574  0.1171 
## 
## Note: contrasts are still on the 0.001(mu + 0.001) scale
## Model below
m4 <- lm(sqrt(Ephedra.below+0.001) ~ test * brome.biomass, data=biomass)
anova(m4)
## Analysis of Variance Table
## 
## Response: sqrt(Ephedra.below + 0.001)
##                     Df   Sum Sq    Mean Sq F value    Pr(>F)    
## test                 6 0.012375 0.00206250  3.9241 0.0009997 ***
## brome.biomass        1 0.000006 0.00000634  0.0121 0.9126479    
## test:brome.biomass   6 0.002439 0.00040654  0.7735 0.5916155    
## Residuals          196 0.103017 0.00052560                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Germination patterns

recruit
##      ID Treatment   Lvl Rep Density ephedra.emergence branching fluoro
## 1     5   clipped  once   1       0                 0         0 0.0000
## 2    10   clipped  once   2       0                 1         2 0.3215
## 3    13   clipped  once   3       0                 1         6 0.7433
## 4    17   clipped  once   4       0                 0         0 0.0000
## 5    23   clipped  once   5       0                 0         0 0.0000
## 6    26   clipped  once   6       0                 0         0 0.0000
## 7    35   clipped  once   7       0                 0         0 0.0000
## 8    39   clipped  once   8       0                 1         4 0.6366
## 9    44   clipped  once   9       0                 0         0 0.0000
## 10   48   clipped  once  10       0                 0         0 0.0000
## 11   53   clipped  once  11       0                 2         8 0.7806
## 12   56   clipped  once  12       0                 0         0 0.0000
## 13   64   clipped  once  13       0                 0         0 0.0000
## 14   69   clipped  once  14       0                 0         0 0.0000
## 15   74   clipped  once  15       0                 0         0 0.0000
## 16   76   clipped  once  16       0                 0         0 0.0000
## 17   81   clipped  once  17       0                 0         0 0.0000
## 18   86   clipped  once  18       0                 0         0 0.0000
## 19   92   clipped  once  19       0                 0         0 0.0000
## 20   96   clipped  once  20       0                 0         0 0.0000
## 21  105   clipped twice   1       0                 0         0 0.0000
## 22  110   clipped twice   2       0                 1         8 0.7619
## 23  113   clipped twice   3       0                 1         5 0.8012
## 24  117   clipped twice   4       0                 1         4 0.7447
## 25  123   clipped twice   5       0                 2         5 0.7471
## 26  126   clipped twice   6       0                 0         0 0.0000
## 27  135   clipped twice   7       0                 1         4 0.5985
## 28  139   clipped twice   8       0                 1         5 0.7935
## 29  144   clipped twice   9       0                 0         0 0.0000
## 30  148   clipped twice  10       0                 1         6 0.6318
## 31  153   clipped twice  11       0                 1         6 0.6807
## 32  156   clipped twice  12       0                 0         0 0.0000
## 33  164   clipped twice  13       0                 0         0 0.0000
## 34  169   clipped twice  14       0                 0         0 0.0000
## 35  174   clipped twice  15       0                 0         0 0.0000
## 36  176   clipped twice  16       0                 1         4 0.7650
## 37  181   clipped twice  17       0                 0         0 0.0000
## 38  186   clipped twice  18       0                 0         0 0.0000
## 39  192   clipped twice  19       0                 0         0 0.0000
## 40  196   clipped twice  20       0                 0         0 0.0000
## 41    4   clipped  once   1       2                 0         0 0.0000
## 42    9   clipped  once   2       2                 0         0 0.0000
## 43   15   clipped  once   3       2                 0         0 0.0000
## 44   20   clipped  once   4       2                 0         0 0.0000
## 45   21   clipped  once   5       2                 0         0 0.0000
## 46   28   clipped  once   6       2                 0         0 0.0000
## 47   34   clipped  once   7       2                 0         0 0.0000
## 48   38   clipped  once   8       2                 0         0 0.0000
## 49   42   clipped  once   9       2                 0         0 0.0000
## 50   47   clipped  once  10       2                 0         0 0.0000
## 51   52   clipped  once  11       2                 0         0 0.0000
## 52   60   clipped  once  12       2                 0         0 0.0000
## 53   63   clipped  once  13       2                 0         0 0.0000
## 54   70   clipped  once  14       2                 0         0 0.0000
## 55   71   clipped  once  15       2                 1         6 0.7615
## 56   80   clipped  once  16       2                 2         7 0.7943
## 57   83   clipped  once  17       2                 0         0 0.0000
## 58   88   clipped  once  18       2                 0         0 0.0000
## 59   91   clipped  once  19       2                 0         0 0.0000
## 60   98   clipped  once  20       2                 0         0 0.0000
## 61  104   clipped twice   1       2                 1         6 0.6954
## 62  109   clipped twice   2       2                 0         0 0.0000
## 63  115   clipped twice   3       2                 1         4 0.7570
## 64  120   clipped twice   4       2                 0         0 0.0000
## 65  121   clipped twice   5       2                 0         0 0.0000
## 66  128   clipped twice   6       2                 0         0 0.0000
## 67  134   clipped twice   7       2                 0         0 0.0000
## 68  138   clipped twice   8       2                 0         0 0.0000
## 69  142   clipped twice   9       2                 0         0 0.0000
## 70  147   clipped twice  10       2                 0         0 0.0000
## 71  152   clipped twice  11       2                 1         4 0.7681
## 72  160   clipped twice  12       2                 0         0 0.0000
## 73  163   clipped twice  13       2                 0         0 0.0000
## 74  170   clipped twice  14       2                 1         6 0.7063
## 75  171   clipped twice  15       2                 0         0 0.0000
## 76  180   clipped twice  16       2                 1         4 0.7995
## 77  183   clipped twice  17       2                 0         0 0.0000
## 78  188   clipped twice  18       2                 0         0 0.0000
## 79  191   clipped twice  19       2                 0         0 0.0000
## 80  198   clipped twice  20       2                 0         0 0.0000
## 81    3   clipped  once   1       5                 1         3 0.6416
## 82    8   clipped  once   2       5                 0         0 0.0000
## 83   14   clipped  once   3       5                 1         4 0.7920
## 84   18   clipped  once   4       5                 0         0 0.0000
## 85   22   clipped  once   5       5                 0         0 0.0000
## 86   29   clipped  once   6       5                 1         5 0.6169
## 87   32   clipped  once   7       5                 0         0 0.0000
## 88   40   clipped  once   8       5                 1         4 0.6732
## 89   41   clipped  once   9       5                 2         8 0.7775
## 90   49   clipped  once  10       5                 1         5 0.8054
## 91   54   clipped  once  11       5                 2         4 0.7938
## 92   59   clipped  once  12       5                 1         3 0.7967
## 93   62   clipped  once  13       5                 1         5 0.7612
## 94   66   clipped  once  14       5                 1         6 0.7740
## 95   73   clipped  once  15       5                 1        11 0.7853
## 96   77   clipped  once  16       5                 0         0 0.0000
## 97   85   clipped  once  17       5                 0         0 0.0000
## 98   87   clipped  once  18       5                 1         6 0.7532
## 99   95   clipped  once  19       5                 0         0 0.0000
## 100  97   clipped  once  20       5                 1         5 0.7839
## 101 103   clipped twice   1       5                 2         6 0.7245
## 102 108   clipped twice   2       5                 2         6 0.7800
## 103 114   clipped twice   3       5                 0         0 0.0000
## 104 118   clipped twice   4       5                 0         0 0.0000
## 105 122   clipped twice   5       5                 1         4 0.7698
## 106 129   clipped twice   6       5                 0         0 0.0000
## 107 132   clipped twice   7       5                 1         6 0.7884
## 108 140   clipped twice   8       5                 0         0 0.0000
## 109 141   clipped twice   9       5                 0         0 0.0000
## 110 149   clipped twice  10       5                 0         0 0.0000
## 111 154   clipped twice  11       5                 0         0 0.0000
## 112 159   clipped twice  12       5                 0         0 0.0000
## 113 162   clipped twice  13       5                 1         4 0.4452
## 114 166   clipped twice  14       5                 1         7 0.6691
## 115 173   clipped twice  15       5                 0         0 0.0000
## 116 177   clipped twice  16       5                 0         0 0.0000
## 117 185   clipped twice  17       5                 1         4 0.7774
## 118 187   clipped twice  18       5                 0         0 0.0000
## 119 195   clipped twice  19       5                 1         5 0.7694
## 120 197   clipped twice  20       5                 1         4 0.7631
## 121   1   clipped  once   1      10                 1         6 0.7867
## 122   6   clipped  once   2      10                 1         3 0.7592
## 123  12   clipped  once   3      10                 0         0 0.0000
## 124  16   clipped  once   4      10                 0         0 0.0000
## 125  25   clipped  once   5      10                 0         0 0.0000
## 126  27   clipped  once   6      10                 0         0 0.0000
## 127  33   clipped  once   7      10                 1         5 0.7789
## 128  36   clipped  once   8      10                 1         7 0.7092
## 129  43   clipped  once   9      10                 0         0 0.0000
## 130  50   clipped  once  10      10                 0         0 0.0000
## 131  55   clipped  once  11      10                 1         4 0.6851
## 132  58   clipped  once  12      10                 0         0 0.0000
## 133  65   clipped  once  13      10                 0         0 0.0000
## 134  68   clipped  once  14      10                 0         0 0.0000
## 135  75   clipped  once  15      10                 1         4 0.7576
## 136  78   clipped  once  16      10                 1         8 0.7499
## 137  84   clipped  once  17      10                 0         0 0.0000
## 138  90   clipped  once  18      10                 0         0 0.0000
## 139  93   clipped  once  19      10                 0         0 0.0000
## 140  99   clipped  once  20      10                 0         0 0.0000
## 141 101   clipped twice   1      10                 0         0 0.0000
## 142 106   clipped twice   2      10                 1         6 0.7842
## 143 112   clipped twice   3      10                 0         0 0.0000
## 144 116   clipped twice   4      10                 0         0 0.0000
## 145 125   clipped twice   5      10                 0         0 0.0000
## 146 127   clipped twice   6      10                 1         5 0.7753
## 147 133   clipped twice   7      10                 0         0 0.0000
## 148 136   clipped twice   8      10                 0         0 0.0000
## 149 143   clipped twice   9      10                 0         0 0.0000
## 150 150   clipped twice  10      10                 1         5 0.7420
## 151 155   clipped twice  11      10                 0         0 0.0000
## 152 158   clipped twice  12      10                 2         7 0.7999
## 153 165   clipped twice  13      10                 0         0 0.0000
## 154 168   clipped twice  14      10                 3         9 0.6319
## 155 175   clipped twice  15      10                 0         0 0.0000
## 156 178   clipped twice  16      10                 2         5 0.5698
## 157 184   clipped twice  17      10                 0         0 0.0000
## 158 190   clipped twice  18      10                 1         4 0.7780
## 159 193   clipped twice  19      10                 0         0 0.0000
## 160 199   clipped twice  20      10                 0         0 0.0000
## 161   2   clipped  once   1      20                 1         7 0.7863
## 162   7   clipped  once   2      20                 0         0 0.0000
## 163  11   clipped  once   3      20                 0         0 0.0000
## 164  19   clipped  once   4      20                 0         0 0.0000
## 165  24   clipped  once   5      20                 0         0 0.0000
## 166  30   clipped  once   6      20                 0         0 0.0000
## 167  31   clipped  once   7      20                 0         0 0.0000
## 168  37   clipped  once   8      20                 0         0 0.0000
## 169  45   clipped  once   9      20                 0         0 0.0000
## 170  46   clipped  once  10      20                 0         0 0.0000
## 171  51   clipped  once  11      20                 0         0 0.0000
## 172  57   clipped  once  12      20                 0         0 0.0000
## 173  61   clipped  once  13      20                 0         0 0.0000
## 174  67   clipped  once  14      20                 0         0 0.0000
## 175  72   clipped  once  15      20                 0         0 0.0000
## 176  79   clipped  once  16      20                 0         0 0.0000
## 177  82   clipped  once  17      20                 0         0 0.0000
## 178  89   clipped  once  18      20                 0         0 0.0000
## 179  94   clipped  once  19      20                 0         0 0.0000
## 180 100   clipped  once  20      20                 1         4 0.6715
## 181 102   clipped twice   1      20                 0         0 0.0000
## 182 107   clipped twice   2      20                 0         0 0.0000
## 183 111   clipped twice   3      20                 0         0 0.0000
## 184 119   clipped twice   4      20                 0         0 0.0000
## 185 124   clipped twice   5      20                 0         0 0.0000
## 186 130   clipped twice   6      20                 1         5 0.5799
## 187 131   clipped twice   7      20                 0         0 0.0000
## 188 137   clipped twice   8      20                 0         0 0.0000
## 189 145   clipped twice   9      20                 1         3 0.7009
## 190 146   clipped twice  10      20                 0         0 0.0000
## 191 151   clipped twice  11      20                 1         5 0.7652
## 192 157   clipped twice  12      20                 0         0 0.0000
## 193 161   clipped twice  13      20                 0         0 0.0000
## 194 167   clipped twice  14      20                 0         0 0.0000
## 195 172   clipped twice  15      20                 0         0 0.0000
## 196 179   clipped twice  16      20                 0         0 0.0000
## 197 182   clipped twice  17      20                 2         6 0.7488
## 198 189   clipped twice  18      20                 0         0 0.0000
## 199 194   clipped twice  19      20                 0         0 0.0000
## 200 200   clipped twice  20      20                 0         0 0.0000
## 201 205   control  none   1       0                 0         0 0.0000
## 202 210   control  none   2       0                 0         0 0.0000
## 203 213   control  none   3       0                 1         5 0.7908
## 204 217   control  none   4       0                 1         3 0.7910
## 205 223   control  none   5       0                 0         0 0.0000
## 206 226   control  none   6       0                 0         0 0.0000
## 207 235   control  none   7       0                 1         6 0.7779
## 208 239   control  none   8       0                 0         0 0.0000
## 209 244   control  none   9       0                 1         6 0.5830
## 210 248   control  none  10       0                 1         5 0.7768
## 211 253   control  none  11       0                 0         0 0.0000
## 212 256   control  none  12       0                 0         0 0.0000
## 213 264   control  none  13       0                 0         0 0.0000
## 214 269   control  none  14       0                 0         0 0.0000
## 215 274   control  none  15       0                 0         0 0.0000
## 216 276   control  none  16       0                 1         4 0.7781
## 217 281   control  none  17       0                 0         0 0.0000
## 218 286   control  none  18       0                 0         0 0.0000
## 219 292   control  none  19       0                 0         0 0.0000
## 220 296   control  none  20       0                 0         0 0.0000
## 221 204   control  none   1       2                 1         9 0.6990
## 222 209   control  none   2       2                 0         0 0.0000
## 223 215   control  none   3       2                 0         0 0.0000
## 224 220   control  none   4       2                 0         0 0.0000
## 225 221   control  none   5       2                 0         0 0.0000
## 226 228   control  none   6       2                 0         0 0.0000
## 227 234   control  none   7       2                 1         5 0.7909
## 228 238   control  none   8       2                 0         0 0.0000
## 229 242   control  none   9       2                 1         5 0.7632
## 230 247   control  none  10       2                 0         0 0.0000
## 231 252   control  none  11       2                 1         7 0.8060
## 232 260   control  none  12       2                 1         7 0.7774
## 233 263   control  none  13       2                 0         0 0.0000
## 234 270   control  none  14       2                 0         0 0.0000
## 235 271   control  none  15       2                 1         6 0.7727
## 236 280   control  none  16       2                 0         0 0.0000
## 237 283   control  none  17       2                 2         5 0.7937
## 238 288   control  none  18       2                 0         0 0.0000
## 239 291   control  none  19       2                 1         3 0.4486
## 240 298   control  none  20       2                 0         0 0.0000
## 241 203   control  none   1       5                 0         0 0.0000
## 242 208   control  none   2       5                 0         0 0.0000
## 243 214   control  none   3       5                 0         0 0.0000
## 244 218   control  none   4       5                 0         0 0.0000
## 245 222   control  none   5       5                 0         0 0.0000
## 246 229   control  none   6       5                 1         6 0.8044
## 247 232   control  none   7       5                 1         3 0.8003
## 248 240   control  none   8       5                 0         0 0.0000
## 249 241   control  none   9       5                 1         3 0.4088
## 250 249   control  none  10       5                 0         0 0.0000
## 251 254   control  none  11       5                 0         0 0.0000
## 252 259   control  none  12       5                 0         0 0.0000
## 253 262   control  none  13       5                 1         9 0.7871
## 254 266   control  none  14       5                 2         5 0.7579
## 255 273   control  none  15       5                 0         0 0.0000
## 256 277   control  none  16       5                 1         3 0.7850
## 257 285   control  none  17       5                 2         8 0.7973
## 258 287   control  none  18       5                 0         0 0.0000
## 259 295   control  none  19       5                 1         5 0.7066
## 260 297   control  none  20       5                 0         0 0.0000
## 261 201   control  none   1      10                 0         0 0.0000
## 262 206   control  none   2      10                 1         5 0.7773
## 263 212   control  none   3      10                 0         0 0.0000
## 264 216   control  none   4      10                 0         0 0.0000
## 265 225   control  none   5      10                 0         0 0.0000
## 266 227   control  none   6      10                 1         7 0.7974
## 267 233   control  none   7      10                 2         3 0.6053
## 268 236   control  none   8      10                 0         0 0.0000
## 269 243   control  none   9      10                 0         0 0.0000
## 270 250   control  none  10      10                 0         0 0.0000
## 271 255   control  none  11      10                 2         7 0.7887
## 272 258   control  none  12      10                 0         0 0.0000
## 273 265   control  none  13      10                 0         0 0.0000
## 274 268   control  none  14      10                 0         0 0.0000
## 275 275   control  none  15      10                 1         7 0.7880
## 276 278   control  none  16      10                 0         0 0.0000
## 277 284   control  none  17      10                 1         4 0.7938
## 278 290   control  none  18      10                 0         0 0.0000
## 279 293   control  none  19      10                 0         0 0.0000
## 280 299   control  none  20      10                 0         0 0.0000
## 281 202   control  none   1      20                 1         3 0.7360
## 282 207   control  none   2      20                 1         5 0.7544
## 283 211   control  none   3      20                 0         0 0.0000
## 284 219   control  none   4      20                 0         0 0.0000
## 285 224   control  none   5      20                 0         0 0.0000
## 286 230   control  none   6      20                 0         0 0.0000
## 287 231   control  none   7      20                 2         5 0.6865
## 288 237   control  none   8      20                 1         3 0.7434
## 289 245   control  none   9      20                 0         0 0.0000
## 290 246   control  none  10      20                 0         0 0.0000
## 291 251   control  none  11      20                 0         0 0.0000
## 292 257   control  none  12      20                 2         5 0.5452
## 293 261   control  none  13      20                 0         0 0.0000
## 294 267   control  none  14      20                 0         0 0.0000
## 295 272   control  none  15      20                 0         0 0.0000
## 296 279   control  none  16      20                 0         0 0.0000
## 297 282   control  none  17      20                 0         0 0.0000
## 298 289   control  none  18      20                 0         0 0.0000
## 299 294   control  none  19      20                 0         0 0.0000
## 300 300   control  none  20      20                 2         7 0.7728
## 301 305     shade  high   1       0                 0         0 0.0000
## 302 310     shade  high   2       0                 0         0 0.0000
## 303 313     shade  high   3       0                 0         0 0.0000
## 304 317     shade  high   4       0                 1         3 0.6200
## 305 323     shade  high   5       0                 0         0 0.0000
## 306 326     shade  high   6       0                 0         0 0.0000
## 307 335     shade  high   7       0                 0         0 0.0000
## 308 339     shade  high   8       0                 0         0 0.0000
## 309 344     shade  high   9       0                 0         0 0.0000
## 310 348     shade  high  10       0                 0         0 0.0000
## 311 353     shade  high  11       0                 0         0 0.0000
## 312 356     shade  high  12       0                 0         0 0.0000
## 313 364     shade  high  13       0                 0         0 0.0000
## 314 369     shade  high  14       0                 0         0 0.0000
## 315 374     shade  high  15       0                 0         0 0.0000
## 316 376     shade  high  16       0                 0         0 0.0000
## 317 381     shade  high  17       0                 0         0 0.0000
## 318 386     shade  high  18       0                 0         0 0.0000
## 319 392     shade  high  19       0                 0         0 0.0000
## 320 396     shade  high  20       0                 1         3 0.8874
## 321 405     shade   med   1       0                 0         0 0.0000
## 322 410     shade   med   2       0                 0         0 0.0000
## 323 413     shade   med   3       0                 0         0 0.0000
## 324 417     shade   med   4       0                 0         0 0.0000
## 325 423     shade   med   5       0                 0         0 0.0000
## 326 426     shade   med   6       0                 1         8 0.7693
## 327 435     shade   med   7       0                 1         7 0.7306
## 328 439     shade   med   8       0                 0         0 0.0000
## 329 444     shade   med   9       0                 0         0 0.0000
## 330 448     shade   med  10       0                 0         0 0.0000
## 331 453     shade   med  11       0                 0         0 0.0000
## 332 456     shade   med  12       0                 0         0 0.0000
## 333 464     shade   med  13       0                 0         0 0.0000
## 334 469     shade   med  14       0                 0         0 0.0000
## 335 474     shade   med  15       0                 0         0 0.0000
## 336 476     shade   med  16       0                 0         0 0.0000
## 337 481     shade   med  17       0                 0         0 0.0000
## 338 486     shade   med  18       0                 1         7 0.7961
## 339 492     shade   med  19       0                 0         0 0.0000
## 340 496     shade   med  20       0                 0         0 0.0000
## 341 304     shade  high   1       2                 0         0 0.0000
## 342 309     shade  high   2       2                 0         0 0.0000
## 343 315     shade  high   3       2                 0         0 0.0000
## 344 320     shade  high   4       2                 1         4 0.7831
## 345 321     shade  high   5       2                 1         5 0.8014
## 346 328     shade  high   6       2                 0         0 0.0000
## 347 334     shade  high   7       2                 0         0 0.0000
## 348 338     shade  high   8       2                 0         0 0.0000
## 349 342     shade  high   9       2                 0         0 0.0000
## 350 347     shade  high  10       2                 0         0 0.0000
## 351 352     shade  high  11       2                 0         0 0.0000
## 352 360     shade  high  12       2                 0         0 0.0000
## 353 363     shade  high  13       2                 2         5 0.7799
## 354 370     shade  high  14       2                 0         0 0.0000
## 355 371     shade  high  15       2                 0         0 0.0000
## 356 380     shade  high  16       2                 0         0 0.0000
## 357 383     shade  high  17       2                 1         5 0.7620
## 358 388     shade  high  18       2                 0         0 0.0000
## 359 391     shade  high  19       2                 0         0 0.0000
## 360 398     shade  high  20       2                 0         0 0.0000
## 361 404     shade   med   1       2                 0         0 0.0000
## 362 409     shade   med   2       2                 0         0 0.0000
## 363 415     shade   med   3       2                 0         0 0.0000
## 364 420     shade   med   4       2                 0         0 0.0000
## 365 421     shade   med   5       2                 0         0 0.0000
## 366 428     shade   med   6       2                 1         4 0.7959
## 367 434     shade   med   7       2                 0         0 0.0000
## 368 438     shade   med   8       2                 0         0 0.0000
## 369 442     shade   med   9       2                 0         0 0.0000
## 370 447     shade   med  10       2                 0         0 0.0000
## 371 452     shade   med  11       2                 0         0 0.0000
## 372 460     shade   med  12       2                 0         0 0.0000
## 373 463     shade   med  13       2                 0         0 0.0000
## 374 470     shade   med  14       2                 0         0 0.0000
## 375 471     shade   med  15       2                 1         5 0.5438
## 376 480     shade   med  16       2                 0         0 0.0000
## 377 483     shade   med  17       2                 0         0 0.0000
## 378 488     shade   med  18       2                 2         8 0.7381
## 379 491     shade   med  19       2                 0         0 0.0000
## 380 498     shade   med  20       2                 0         0 0.0000
## 381 303     shade  high   1       5                 1         4 0.5240
## 382 308     shade  high   2       5                 1         4 0.7704
## 383 314     shade  high   3       5                 0         0 0.0000
## 384 318     shade  high   4       5                 0         0 0.0000
## 385 322     shade  high   5       5                 0         0 0.0000
## 386 329     shade  high   6       5                 0         0 0.0000
## 387 332     shade  high   7       5                 0         0 0.0000
## 388 340     shade  high   8       5                 0         0 0.0000
## 389 341     shade  high   9       5                 0         0 0.0000
## 390 349     shade  high  10       5                 0         0 0.0000
## 391 354     shade  high  11       5                 0         0 0.0000
## 392 359     shade  high  12       5                 0         0 0.0000
## 393 362     shade  high  13       5                 0         0 0.0000
## 394 366     shade  high  14       5                 0         0 0.0000
## 395 373     shade  high  15       5                 0         0 0.0000
## 396 377     shade  high  16       5                 0         0 0.0000
## 397 385     shade  high  17       5                 0         0 0.0000
## 398 387     shade  high  18       5                 0         0 0.0000
## 399 395     shade  high  19       5                 0         0 0.0000
## 400 397     shade  high  20       5                 0         0 0.0000
## 401 403     shade   med   1       5                 0         0 0.0000
## 402 408     shade   med   2       5                 2         6 0.5096
## 403 414     shade   med   3       5                 0         0 0.0000
## 404 418     shade   med   4       5                 0         0 0.0000
## 405 422     shade   med   5       5                 0         0 0.0000
## 406 429     shade   med   6       5                 0         0 0.0000
## 407 432     shade   med   7       5                 0         0 0.0000
## 408 440     shade   med   8       5                 1         5 0.8030
## 409 441     shade   med   9       5                 0         0 0.0000
## 410 449     shade   med  10       5                 0         0 0.0000
## 411 454     shade   med  11       5                 0         0 0.0000
## 412 459     shade   med  12       5                 0         0 0.0000
## 413 462     shade   med  13       5                 1         7 0.7493
## 414 466     shade   med  14       5                 0         0 0.0000
## 415 473     shade   med  15       5                 0         0 0.0000
## 416 477     shade   med  16       5                 0         0 0.0000
## 417 485     shade   med  17       5                 0         0 0.0000
## 418 487     shade   med  18       5                 0         0 0.0000
## 419 495     shade   med  19       5                 0         0 0.0000
## 420 497     shade   med  20       5                 0         0 0.0000
## 421 301     shade  high   1      10                 1         5 0.7900
## 422 306     shade  high   2      10                 0         0 0.0000
## 423 312     shade  high   3      10                 0         0 0.0000
## 424 316     shade  high   4      10                 0         0 0.0000
## 425 325     shade  high   5      10                 0         0 0.0000
## 426 327     shade  high   6      10                 0         0 0.0000
## 427 333     shade  high   7      10                 0         0 0.0000
## 428 336     shade  high   8      10                 0         0 0.0000
## 429 343     shade  high   9      10                 0         0 0.0000
## 430 350     shade  high  10      10                 0         0 0.0000
## 431 355     shade  high  11      10                 0         0 0.0000
## 432 358     shade  high  12      10                 0         0 0.0000
## 433 365     shade  high  13      10                 0         0 0.0000
## 434 368     shade  high  14      10                 0         0 0.0000
## 435 375     shade  high  15      10                 0         0 0.0000
## 436 378     shade  high  16      10                 0         0 0.0000
## 437 384     shade  high  17      10                 0         0 0.0000
## 438 390     shade  high  18      10                 0         0 0.0000
## 439 393     shade  high  19      10                 0         0 0.0000
## 440 399     shade  high  20      10                 0         0 0.0000
## 441 401     shade   med   1      10                 1         7 0.7954
## 442 406     shade   med   2      10                 0         0 0.0000
## 443 412     shade   med   3      10                 0         0 0.0000
## 444 416     shade   med   4      10                 0         0 0.0000
## 445 425     shade   med   5      10                 0         0 0.0000
## 446 427     shade   med   6      10                 0         0 0.0000
## 447 433     shade   med   7      10                 0         0 0.0000
## 448 436     shade   med   8      10                 0         0 0.0000
## 449 443     shade   med   9      10                 0         0 0.0000
## 450 450     shade   med  10      10                 0         0 0.0000
## 451 455     shade   med  11      10                 0         0 0.0000
## 452 458     shade   med  12      10                 0         0 0.0000
## 453 465     shade   med  13      10                 0         0 0.0000
## 454 468     shade   med  14      10                 0         0 0.0000
## 455 475     shade   med  15      10                 0         0 0.0000
## 456 478     shade   med  16      10                 0         0 0.0000
## 457 484     shade   med  17      10                 0         0 0.0000
## 458 490     shade   med  18      10                 0         0 0.0000
## 459 493     shade   med  19      10                 0         0 0.0000
## 460 499     shade   med  20      10                 0         0 0.0000
## 461 302     shade  high   1      20                 0         0 0.0000
## 462 307     shade  high   2      20                 0         0 0.0000
## 463 311     shade  high   3      20                 0         0 0.0000
## 464 319     shade  high   4      20                 0         0 0.0000
## 465 324     shade  high   5      20                 0         0 0.0000
## 466 330     shade  high   6      20                 0         0 0.0000
## 467 331     shade  high   7      20                 0         0 0.0000
## 468 337     shade  high   8      20                 0         0 0.0000
## 469 345     shade  high   9      20                 0         0 0.0000
## 470 346     shade  high  10      20                 1         7 0.7807
## 471 351     shade  high  11      20                 1         4 0.7201
## 472 357     shade  high  12      20                 0         0 0.0000
## 473 361     shade  high  13      20                 0         0 0.0000
## 474 367     shade  high  14      20                 0         0 0.0000
## 475 372     shade  high  15      20                 0         0 0.0000
## 476 379     shade  high  16      20                 0         0 0.0000
## 477 382     shade  high  17      20                 0         0 0.0000
## 478 389     shade  high  18      20                 0         0 0.0000
## 479 394     shade  high  19      20                 0         0 0.0000
## 480 400     shade  high  20      20                 0         0 0.0000
## 481 402     shade   med   1      20                 0         0 0.0000
## 482 407     shade   med   2      20                 0         0 0.0000
## 483 411     shade   med   3      20                 0         0 0.0000
## 484 419     shade   med   4      20                 0         0 0.0000
## 485 424     shade   med   5      20                 0         0 0.0000
## 486 430     shade   med   6      20                 0         0 0.0000
## 487 431     shade   med   7      20                 0         0 0.0000
## 488 437     shade   med   8      20                 0         0 0.0000
## 489 445     shade   med   9      20                 0         0 0.0000
## 490 446     shade   med  10      20                 0         0 0.0000
## 491 451     shade   med  11      20                 0         0 0.0000
## 492 457     shade   med  12      20                 0         0 0.0000
## 493 461     shade   med  13      20                 1         2 0.6052
## 494 467     shade   med  14      20                 0         0 0.0000
## 495 472     shade   med  15      20                 0         0 0.0000
## 496 479     shade   med  16      20                 0         0 0.0000
## 497 482     shade   med  17      20                 0         0 0.0000
## 498 489     shade   med  18      20                 0         0 0.0000
## 499 494     shade   med  19      20                 0         0 0.0000
## 500 500     shade   med  20      20                 0         0 0.0000
## 501 505     water  high   1       0                 1         5 0.7860
## 502 510     water  high   2       0                 1         5 0.7988
## 503 513     water  high   3       0                 1         4 0.8049
## 504 517     water  high   4       0                 2         7 0.7890
## 505 523     water  high   5       0                 0         0 0.0000
## 506 526     water  high   6       0                 1         6 0.7990
## 507 535     water  high   7       0                 0         0 0.0000
## 508 539     water  high   8       0                 0         0 0.0000
## 509 544     water  high   9       0                 1         5 0.8016
## 510 548     water  high  10       0                 0         0 0.0000
## 511 553     water  high  11       0                 0         0 0.0000
## 512 556     water  high  12       0                 0         0 0.0000
## 513 564     water  high  13       0                 1         4 0.3523
## 514 569     water  high  14       0                 0         0 0.0000
## 515 574     water  high  15       0                 1         7 0.7320
## 516 576     water  high  16       0                 0         0 0.0000
## 517 581     water  high  17       0                 0         0 0.0000
## 518 586     water  high  18       0                 0         0 0.0000
## 519 592     water  high  19       0                 1         6 0.8004
## 520 596     water  high  20       0                 0         0 0.0000
## 521 605     water   low   1       0                 1         7 0.8077
## 522 610     water   low   2       0                 0         0 0.0000
## 523 613     water   low   3       0                 1         5 0.7018
## 524 617     water   low   4       0                 1         8 0.7353
## 525 623     water   low   5       0                 0         0 0.0000
## 526 626     water   low   6       0                 1         8 0.7515
## 527 635     water   low   7       0                 1         7 0.7973
## 528 639     water   low   8       0                 0         0 0.0000
## 529 644     water   low   9       0                 0         0 0.0000
## 530 648     water   low  10       0                 1         5 0.7796
## 531 653     water   low  11       0                 0         0 0.0000
## 532 656     water   low  12       0                 0         0 0.0000
## 533 664     water   low  13       0                 0         0 0.0000
## 534 669     water   low  14       0                 2         9 0.7844
## 535 674     water   low  15       0                 0         0 0.0000
## 536 676     water   low  16       0                 0         0 0.0000
## 537 681     water   low  17       0                 0         0 0.0000
## 538 686     water   low  18       0                 0         0 0.0000
## 539 692     water   low  19       0                 0         0 0.0000
## 540 696     water   low  20       0                 0         0 0.0000
## 541 504     water  high   1       2                 0         0 0.0000
## 542 509     water  high   2       2                 0         0 0.0000
## 543 515     water  high   3       2                 0         0 0.0000
## 544 520     water  high   4       2                 0         0 0.0000
## 545 521     water  high   5       2                 1         6 0.5436
## 546 528     water  high   6       2                 0         0 0.0000
## 547 534     water  high   7       2                 1         4 0.6423
## 548 538     water  high   8       2                 0         0 0.0000
## 549 542     water  high   9       2                 1         6 0.7139
## 550 547     water  high  10       2                 0         0 0.0000
## 551 552     water  high  11       2                 1         3 0.6860
## 552 560     water  high  12       2                 0         0 0.0000
## 553 563     water  high  13       2                 0         0 0.0000
## 554 570     water  high  14       2                 0         0 0.0000
## 555 571     water  high  15       2                 0         0 0.0000
## 556 580     water  high  16       2                 2         4 0.5730
## 557 583     water  high  17       2                 1         6 0.7429
## 558 588     water  high  18       2                 1         6 0.7680
## 559 591     water  high  19       2                 1         5 0.6706
## 560 598     water  high  20       2                 0         0 0.0000
## 561 604     water   low   1       2                 1         6 0.6032
## 562 609     water   low   2       2                 0         0 0.0000
## 563 615     water   low   3       2                 0         0 0.0000
## 564 620     water   low   4       2                 0         0 0.0000
## 565 621     water   low   5       2                 0         0 0.0000
## 566 628     water   low   6       2                 1         3 0.7533
## 567 634     water   low   7       2                 0         0 0.0000
## 568 638     water   low   8       2                 0         0 0.0000
## 569 642     water   low   9       2                 1         3 0.1651
## 570 647     water   low  10       2                 1         9 0.7817
## 571 652     water   low  11       2                 0         0 0.0000
## 572 660     water   low  12       2                 0         0 0.0000
## 573 663     water   low  13       2                 1         7 0.7852
## 574 670     water   low  14       2                 1         6 0.7514
## 575 671     water   low  15       2                 0         0 0.0000
## 576 680     water   low  16       2                 0         0 0.0000
## 577 683     water   low  17       2                 1         5 0.7886
## 578 688     water   low  18       2                 0         0 0.0000
## 579 691     water   low  19       2                 0         0 0.0000
## 580 698     water   low  20       2                 1         5 0.8047
## 581 503     water  high   1       5                 1         5 0.7532
## 582 508     water  high   2       5                 0         0 0.0000
## 583 514     water  high   3       5                 1         9 0.7921
## 584 518     water  high   4       5                 1         7 0.7809
## 585 522     water  high   5       5                 1         4 0.7513
## 586 529     water  high   6       5                 0         0 0.0000
## 587 532     water  high   7       5                 0         0 0.0000
## 588 540     water  high   8       5                 0         0 0.0000
## 589 541     water  high   9       5                 0         0 0.0000
## 590 549     water  high  10       5                 0         0 0.0000
## 591 554     water  high  11       5                 0         0 0.0000
## 592 559     water  high  12       5                 0         0 0.0000
## 593 562     water  high  13       5                 0         0 0.0000
## 594 566     water  high  14       5                 0         0 0.0000
## 595 573     water  high  15       5                 0         0 0.0000
## 596 577     water  high  16       5                 0         0 0.0000
## 597 585     water  high  17       5                 0         0 0.0000
## 598 587     water  high  18       5                 0         0 0.0000
## 599 595     water  high  19       5                 0         0 0.0000
## 600 597     water  high  20       5                 0         0 0.0000
## 601 603     water   low   1       5                 0         0 0.0000
## 602 608     water   low   2       5                 0         0 0.0000
## 603 614     water   low   3       5                 0         0 0.0000
## 604 618     water   low   4       5                 0         0 0.0000
## 605 622     water   low   5       5                 0         0 0.0000
## 606 629     water   low   6       5                 1         5 0.7865
## 607 632     water   low   7       5                 0         0 0.0000
## 608 640     water   low   8       5                 0         0 0.0000
## 609 641     water   low   9       5                 1         5 0.7016
## 610 649     water   low  10       5                 0         0 0.0000
## 611 654     water   low  11       5                 0         0 0.0000
## 612 659     water   low  12       5                 0         0 0.0000
## 613 662     water   low  13       5                 0         0 0.0000
## 614 666     water   low  14       5                 0         0 0.0000
## 615 673     water   low  15       5                 0         0 0.0000
## 616 677     water   low  16       5                 0         0 0.0000
## 617 685     water   low  17       5                 1         5 0.7909
## 618 687     water   low  18       5                 0         0 0.0000
## 619 695     water   low  19       5                 1         6 0.8080
## 620 697     water   low  20       5                 0         0 0.0000
## 621 501     water  high   1      10                 0         0 0.0000
## 622 506     water  high   2      10                 0         0 0.0000
## 623 512     water  high   3      10                 0         0 0.0000
## 624 516     water  high   4      10                 1         4 0.8079
## 625 525     water  high   5      10                 0         0 0.0000
## 626 527     water  high   6      10                 0         0 0.0000
## 627 533     water  high   7      10                 2         9 0.7831
## 628 536     water  high   8      10                 0         0 0.0000
## 629 543     water  high   9      10                 1         7 0.7919
## 630 550     water  high  10      10                 0         0 0.0000
## 631 555     water  high  11      10                 0         0 0.0000
## 632 558     water  high  12      10                 1         5 0.7547
## 633 565     water  high  13      10                 0         0 0.0000
## 634 568     water  high  14      10                 0         0 0.0000
## 635 575     water  high  15      10                 0         0 0.0000
## 636 578     water  high  16      10                 0         0 0.0000
## 637 584     water  high  17      10                 0         0 0.0000
## 638 590     water  high  18      10                 0         0 0.0000
## 639 593     water  high  19      10                 0         0 0.0000
## 640 599     water  high  20      10                 0         0 0.0000
## 641 601     water   low   1      10                 1         7 0.7586
## 642 606     water   low   2      10                 1         5 0.8027
## 643 612     water   low   3      10                 0         0 0.0000
## 644 616     water   low   4      10                 0         0 0.0000
## 645 625     water   low   5      10                 0         0 0.0000
## 646 627     water   low   6      10                 0         0 0.0000
## 647 633     water   low   7      10                 1         6 0.7595
## 648 636     water   low   8      10                 1        10 0.7776
## 649 643     water   low   9      10                 0         0 0.0000
## 650 650     water   low  10      10                 0         0 0.0000
## 651 655     water   low  11      10                 0         0 0.0000
## 652 658     water   low  12      10                 0         0 0.0000
## 653 665     water   low  13      10                 1         7 0.6986
## 654 668     water   low  14      10                 0         0 0.0000
## 655 675     water   low  15      10                 0         0 0.0000
## 656 678     water   low  16      10                 1         7 0.8063
## 657 684     water   low  17      10                 0         0 0.0000
## 658 690     water   low  18      10                 1         7 0.7980
## 659 693     water   low  19      10                 0         0 0.0000
## 660 699     water   low  20      10                 0         0 0.0000
## 661 502     water  high   1      20                 1         7 0.7895
## 662 507     water  high   2      20                 1         7 0.8028
## 663 511     water  high   3      20                 0         0 0.0000
## 664 519     water  high   4      20                 0         0 0.0000
## 665 524     water  high   5      20                 2         8 0.7687
## 666 530     water  high   6      20                 0         0 0.0000
## 667 531     water  high   7      20                 1         5 0.7742
## 668 537     water  high   8      20                 1         7 0.8034
## 669 545     water  high   9      20                 0         0 0.0000
## 670 546     water  high  10      20                 0         0 0.0000
## 671 551     water  high  11      20                 0         0 0.0000
## 672 557     water  high  12      20                 1         2 0.7315
## 673 561     water  high  13      20                 0         0 0.0000
## 674 567     water  high  14      20                 0         0 0.0000
## 675 572     water  high  15      20                 0         0 0.0000
## 676 579     water  high  16      20                 0         0 0.0000
## 677 582     water  high  17      20                 0         0 0.0000
## 678 589     water  high  18      20                 0         0 0.0000
## 679 594     water  high  19      20                 0         0 0.0000
## 680 600     water  high  20      20                 0         0 0.0000
## 681 602     water   low   1      20                 0         0 0.0000
## 682 607     water   low   2      20                 1         6 0.7758
## 683 611     water   low   3      20                 0         0 0.0000
## 684 619     water   low   4      20                 1         7 0.8032
## 685 624     water   low   5      20                 1         5 0.8062
## 686 630     water   low   6      20                 0         0 0.0000
## 687 631     water   low   7      20                 0         0 0.0000
## 688 637     water   low   8      20                 0         0 0.0000
## 689 645     water   low   9      20                 0         0 0.0000
## 690 646     water   low  10      20                 1         5 0.7975
## 691 651     water   low  11      20                 0         0 0.0000
## 692 657     water   low  12      20                 0         0 0.0000
## 693 661     water   low  13      20                 0         0 0.0000
## 694 667     water   low  14      20                 0         0 0.0000
## 695 672     water   low  15      20                 0         0 0.0000
## 696 679     water   low  16      20                 0         0 0.0000
## 697 682     water   low  17      20                 0         0 0.0000
## 698 689     water   low  18      20                 0         0 0.0000
## 699 694     water   low  19      20                 0         0 0.0000
## 700 700     water   low  20      20                 0         0 0.0000
##     brome.begin brome.prop.begin ephedra.begin ephedra.end brome.respawn
## 1             0                0             0           0             0
## 2             0                0             1           1             0
## 3             0                0             1           1             0
## 4             0                0             0           0             0
## 5             0                0             1           0             0
## 6             0                0             0           0             0
## 7             0                0             0           0             0
## 8             0                0             1           1             2
## 9             0                0             0           0             0
## 10            0                0             0           0             0
## 11            0                0             1           1             0
## 12            0                0             0           0             0
## 13            0                0             0           0             0
## 14            0                0             0           0             0
## 15            0                0             1           0             0
## 16            0                0             1           0             0
## 17            0                0             0           0             0
## 18            0                0             1           1             0
## 19            0                0             0           0             0
## 20            0                0             0           0             0
## 21            0                0             0           0             0
## 22            0                0             1           1             0
## 23            0                0             1           1             0
## 24            0                0             1           1             0
## 25            0                0             1           1             0
## 26            0                0             1           1             0
## 27            0                0             1           1             0
## 28            0                0             1           1             0
## 29            0                0             1           1             0
## 30            0                0             1           1             0
## 31            0                0             1           1             0
## 32            0                0             0           0             0
## 33            0                0             1           1             0
## 34            0                0             0           0             0
## 35            0                0             0           0             0
## 36            0                0             1           1             0
## 37            0                0             0           0             0
## 38            0                0             0           0             0
## 39            0                0             0           0             0
## 40            0                0             0           0             0
## 41            1               50             0           0             1
## 42            2              100             0           0             0
## 43            1               50             0           0             1
## 44            2              100             0           0             2
## 45            0                0             0           0             0
## 46            1               50             0           0             1
## 47            2              100             0           0             1
## 48            2              100             0           0             0
## 49            1               50             1           0             0
## 50            1               50             0           0             0
## 51            1               50             0           0             0
## 52            2              100             0           0             2
## 53            2              100             0           0             2
## 54            1               50             1           1             2
## 55            1               50             1           1             0
## 56            2              100             1           1             0
## 57            2              100             0           0             0
## 58            0                0             1           0             0
## 59            0                0             1           0             0
## 60            0                0             0           0             0
## 61            0                0             1           1             0
## 62            1               50             0           0             0
## 63            2              100             1           1             1
## 64            2              100             0           0             1
## 65            2              100             0           0             0
## 66            1               50             0           0             0
## 67            0                0             1           1             1
## 68            2              100             0           0             0
## 69            2              100             0           0             1
## 70            1               50             0           0             1
## 71            2              100             1           1             0
## 72            2              100             0           0             1
## 73            0                0             1           1             0
## 74            2              100             1           1             2
## 75            2              100             0           0             0
## 76            1               50             1           1             0
## 77            1               50             0           0             0
## 78            2              100             0           0             2
## 79            2              100             0           0             0
## 80            0                0             0           0             0
## 81            4               80             1           1             0
## 82            5              100             0           0             0
## 83            5              100             1           1             1
## 84            5              100             0           0             1
## 85            3               60             1           1             0
## 86            4               80             1           1             0
## 87            2               40             1           1             0
## 88            5              100             1           1             1
## 89            4               80             1           1             2
## 90            3               60             1           1             0
## 91            2               40             1           1             1
## 92            1               20             1           1             1
## 93            3               60             1           1             1
## 94            4               80             1           1             0
## 95            2               40             1           1             0
## 96            5              100             0           0             0
## 97            1               20             0           0             2
## 98            5              100             1           1             1
## 99            3               60             1           0             0
## 100           4               80             1           1             1
## 101           5              100             1           1             3
## 102           5              100             1           1             0
## 103           4               80             0           0             2
## 104           3               60             0           0             0
## 105           4               80             1           1             0
## 106           5              100             1           1             1
## 107           2               40             1           1             1
## 108           5              100             1           0             0
## 109           2               40             0           0             0
## 110           4               80             0           0             0
## 111           3               60             0           0             0
## 112           3               60             0           0             2
## 113           0                0             1           1             0
## 114           1               20             0           0             2
## 115           3               60             0           0             3
## 116           5              100             0           0             0
## 117           5              100             1           1             2
## 118           5              100             0           0             0
## 119           4               80             1           1             2
## 120           5              100             0           0             1
## 121           3               30             1           1             0
## 122           5               50             1           1             0
## 123           8               80             0           0             0
## 124           4               40             0           0             0
## 125           8               80             0           0             0
## 126           9               90             0           0             0
## 127          10              100             1           1             2
## 128           5               50             1           1             0
## 129           7               70             0           0             0
## 130           9               90             1           0             1
## 131           3               30             1           1             0
## 132           7               70             1           0             2
## 133           4               40             0           0             0
## 134           3               30             0           0             0
## 135           9               90             1           1             3
## 136           7               70             1           1             0
## 137           6               60             0           0             0
## 138           7               70             1           0             0
## 139           4               40             0           0             1
## 140           0                0             0           0             0
## 141           5               50             0           0             2
## 142           7               70             1           1             0
## 143           7               70             0           0             2
## 144           6               60             0           0             3
## 145           9               90             0           0             3
## 146           6               60             1           1             0
## 147           8               80             0           0             0
## 148           3               30             0           0             1
## 149           8               80             0           0             0
## 150           9               90             1           1             1
## 151           9               90             0           0             0
## 152           5               50             1           1             1
## 153           7               70             1           0             1
## 154          10              100             1           1             0
## 155           8               80             0           0             2
## 156           6               60             1           1             1
## 157           7               70             0           0             0
## 158          10              100             1           1             3
## 159           7               70             0           0             0
## 160           3               30             0           0             2
## 161           8               40             1           1             2
## 162          11               55             0           0             0
## 163          11               55             1           0             3
## 164           9               45             0           0             1
## 165          11               55             0           0             4
## 166           9               45             0           0             3
## 167          13               65             1           0             2
## 168          11               55             1           1             0
## 169           0                0             0           0             0
## 170          13               65             0           0             0
## 171          10               50             0           0             0
## 172           8               40             0           0             0
## 173          10               50             1           1             0
## 174           8               40             0           0             0
## 175           8               40             0           0             0
## 176           9               45             1           0             2
## 177          11               55             0           0             1
## 178          14               70             0           0             2
## 179          10               50             0           0             4
## 180          14               70             1           1             2
## 181           9               45             0           0             2
## 182           9               45             0           0             0
## 183          15               75             0           0             3
## 184          14               70             0           0             3
## 185           9               45             1           1             1
## 186          13               65             1           1             1
## 187          12               60             0           0             2
## 188           1                5             0           0             0
## 189          17               85             0           0             3
## 190          12               60             0           0             3
## 191           8               40             1           0             2
## 192          11               55             1           1             1
## 193          16               80             1           0             0
## 194          10               50             1           1             3
## 195          14               70             0           0             0
## 196          11               55             0           0             2
## 197          10               50             1           1             0
## 198          12               60             0           0             2
## 199           9               45             0           0             4
## 200          13               65             0           0             3
## 201           0                0             1           0             0
## 202           0                0             1           1             0
## 203           0                0             1           1             0
## 204           0                0             1           1             0
## 205           0                0             0           0             0
## 206           0                0             0           0             0
## 207           0                0             1           1             0
## 208           0                0             0           0             0
## 209           0                0             1           1             0
## 210           0                0             1           1             0
## 211           0                0             1           1             0
## 212           0                0             0           0             0
## 213           0                0             1           1             1
## 214           0                0             0           0             0
## 215           0                0             1           0             0
## 216           0                0             1           1             0
## 217           0                0             1           0             0
## 218           0                0             0           0             0
## 219           0                0             0           0             0
## 220           0                0             1           0             0
## 221           2              100             1           1             0
## 222           2              100             0           0             0
## 223           2              100             1           0             0
## 224           2              100             0           0             0
## 225           1               50             0           0             0
## 226           1               50             0           0             1
## 227           2              100             1           1             2
## 228           2              100             1           1             0
## 229           1               50             1           1             0
## 230           1               50             1           1             0
## 231           2              100             1           1             0
## 232           2              100             1           1             0
## 233           1               50             0           0             0
## 234           2              100             0           0             0
## 235           0                0             0           0             0
## 236           2              100             0           0             0
## 237           1               50             1           1             0
## 238           1               50             0           0             0
## 239           1               50             1           0             1
## 240           1               50             0           0             0
## 241           4               80             0           0             0
## 242           3               60             0           0             3
## 243           5              100             0           0             0
## 244           4               80             0           0             1
## 245           3               60             0           0             1
## 246           2               40             1           1             1
## 247           4               80             1           1             1
## 248           3               60             1           0             3
## 249           3               60             1           1             2
## 250           2               40             1           0             0
## 251           5              100             0           0             2
## 252           3               60             0           0             0
## 253           5              100             1           1             0
## 254           3               60             1           1             1
## 255           4               80             1           0             0
## 256           3               60             1           1             0
## 257           4               80             1           0             0
## 258           3               60             0           0             0
## 259           5              100             1           1             2
## 260           5              100             0           0             1
## 261           9               90             0           0             1
## 262           5               50             1           1             1
## 263           5               50             0           0             2
## 264           6               60             0           0             0
## 265           5               50             1           0             0
## 266          10              100             1           1             2
## 267           7               70             1           1             0
## 268           4               40             0           0             0
## 269           8               80             1           0             0
## 270           5               50             0           0             0
## 271           7               70             1           1             0
## 272           3               30             0           0             0
## 273           7               70             1           0             0
## 274           8               80             0           0             0
## 275           5               50             1           1             0
## 276           7               70             0           0             0
## 277           8               80             1           1             1
## 278          10              100             0           0             1
## 279           4               40             1           0             0
## 280           7               70             0           0             1
## 281          10               50             1           1             2
## 282          10               50             1           1             2
## 283          14               70             0           0             3
## 284          10               50             0           0             1
## 285          12               60             0           0             2
## 286          10               50             0           0             2
## 287          12               60             1           1             0
## 288          10               50             1           1             0
## 289           7               35             0           0             1
## 290          10               50             0           0             5
## 291          14               70             1           0             2
## 292           6               30             1           1             0
## 293           9               45             0           0             0
## 294          14               70             0           0             0
## 295           9               45             1           0             0
## 296          12               60             0           0             2
## 297          15               75             1           0             0
## 298          12               60             1           0             1
## 299           8               40             1           0             2
## 300          13               65             1           1             0
## 301           0                0             0           0             0
## 302           0                0             1           1             0
## 303           0                0             0           0             0
## 304           0                0             1           1             0
## 305           0                0             0           0             0
## 306           0                0             1           1             0
## 307           0                0             0           0             0
## 308           0                0             0           0             0
## 309           0                0             1           1             0
## 310           0                0             0           0             0
## 311           0                0             0           0             0
## 312           0                0             0           0             0
## 313           0                0             1           1             0
## 314           0                0             0           0             0
## 315           0                0             0           0             0
## 316           0                0             0           0             0
## 317           0                0             1           1             0
## 318           0                0             0           0             0
## 319           0                0             1           0             0
## 320           0                0             1           1             0
## 321           0                0             0           0             0
## 322           0                0             0           0             0
## 323           0                0             0           0             0
## 324           0                0             0           0             0
## 325           0                0             0           0             0
## 326           0                0             1           0             0
## 327           0                0             1           1             0
## 328           0                0             1           0             0
## 329           0                0             0           0             0
## 330           0                0             1           0             0
## 331           0                0             0           0             0
## 332           0                0             0           0             0
## 333           0                0             0           0             0
## 334           0                0             0           0             0
## 335           0                0             0           0             0
## 336           0                0             1           0             0
## 337           0                0             0           0             0
## 338           0                0             1           1             0
## 339           0                0             1           0             0
## 340           0                0             0           0             0
## 341           2              100             0           0             0
## 342           1               50             0           0             0
## 343           2              100             0           0             0
## 344           2              100             1           1             0
## 345           2              100             1           1             0
## 346           2              100             0           0             0
## 347           2              100             0           0             0
## 348           2              100             1           1             0
## 349           1               50             0           0             0
## 350           2              100             0           0             2
## 351           2              100             0           0             0
## 352           2              100             0           0             0
## 353           2              100             1           1             0
## 354           2              100             0           0             0
## 355           2              100             1           1             1
## 356           2              100             0           0             0
## 357           2              100             0           0             0
## 358           2              100             1           1             0
## 359           2              100             0           0             0
## 360           2              100             0           0             0
## 361           1               50             1           0             0
## 362           1               50             0           0             0
## 363           2              100             0           0             0
## 364           0                0             0           0             0
## 365           1               50             1           0             0
## 366           1               50             1           1             0
## 367           0                0             0           0             0
## 368           2              100             0           0             0
## 369           1               50             1           1             0
## 370           2              100             1           0             0
## 371           1               50             0           0             0
## 372           2              100             1           1             0
## 373           2              100             0           0             0
## 374           2              100             0           0             0
## 375           1               50             1           1             0
## 376           2              100             0           0             0
## 377           1               50             1           1             0
## 378           0                0             1           1             0
## 379           0                0             0           0             0
## 380           0                0             0           0             0
## 381           4               80             1           1             0
## 382           5              100             1           1             0
## 383           4               80             1           1             0
## 384           3               60             1           1             0
## 385           4               80             1           1             0
## 386           4               80             0           0             0
## 387           4               80             0           0             0
## 388           4               80             0           0             0
## 389           3               60             0           0             0
## 390           5              100             1           1             0
## 391           4               80             0           0             0
## 392           5              100             0           0             0
## 393           2               40             1           1             0
## 394           4               80             0           0             2
## 395           4               80             0           0             0
## 396           4               80             0           0             0
## 397           5              100             0           0             0
## 398           3               60             1           1             0
## 399           3               60             1           1             0
## 400           4               80             0           0             0
## 401           3               60             0           0             0
## 402           3               60             1           1             0
## 403           1               20             1           1             0
## 404           4               80             1           1             0
## 405           3               60             0           0             0
## 406           5              100             1           0             0
## 407           5              100             0           0             3
## 408           2               40             1           1             0
## 409           3               60             0           0             0
## 410           3               60             0           0             2
## 411           4               80             0           0             0
## 412           4               80             0           0             0
## 413           4               80             1           1             0
## 414           3               60             0           0             0
## 415           0                0             1           0             0
## 416           1               20             0           0             0
## 417           4               80             0           0             0
## 418           3               60             0           0             0
## 419           4               80             0           0             0
## 420           0                0             0           0             0
## 421          10              100             1           1             1
## 422           7               70             0           0             0
## 423           7               70             0           0             0
## 424           7               70             0           0             0
## 425           3               30             0           0             0
## 426           7               70             0           0             0
## 427           8               80             1           1             0
## 428           7               70             1           1             0
## 429           8               80             0           0             0
## 430           7               70             0           0             0
## 431           5               50             0           0             0
## 432           5               50             1           1             0
## 433           7               70             0           0             0
## 434           6               60             0           0             0
## 435           5               50             0           0             0
## 436           8               80             1           1             0
## 437           7               70             0           0             0
## 438           4               40             0           0             0
## 439           5               50             1           1             0
## 440           9               90             1           1             0
## 441           5               50             1           1             0
## 442          10              100             0           0             1
## 443           6               60             0           0             0
## 444           8               80             1           1             0
## 445           6               60             0           0             0
## 446           6               60             0           0             0
## 447           6               60             0           0             0
## 448           7               70             0           0             1
## 449           7               70             0           0             1
## 450           6               60             0           0             0
## 451           5               50             0           0             1
## 452           5               50             0           0             0
## 453           7               70             0           0             0
## 454           7               70             1           1             0
## 455           7               70             0           0             0
## 456           4               40             0           0             0
## 457           4               40             0           0             0
## 458           8               80             0           0             0
## 459           5               50             0           0             0
## 460           5               50             0           0             0
## 461           8               40             0           0             0
## 462          14               70             1           1             0
## 463          11               55             0           0             0
## 464          12               60             0           0             0
## 465          14               70             1           1             0
## 466           9               45             0           0             0
## 467          11               55             1           1             0
## 468           8               40             0           0             0
## 469          12               60             0           0             0
## 470          14               70             1           1             2
## 471          12               60             1           1             3
## 472          13               65             0           0             3
## 473           8               40             0           0             0
## 474          12               60             1           1             0
## 475          10               50             0           0             0
## 476          16               80             1           1             0
## 477          13               65             0           0             1
## 478          11               55             0           0             0
## 479          12               60             1           1             0
## 480           9               45             0           0             0
## 481           8               40             0           0             0
## 482          12               60             0           0             0
## 483           9               45             0           0             0
## 484          12               60             0           0             1
## 485           8               40             0           0             0
## 486          13               65             0           0             1
## 487           9               45             0           0             0
## 488           7               35             0           0             1
## 489           7               35             0           0             0
## 490           3               15             0           0             0
## 491           6               30             1           1             0
## 492           8               40             0           0             0
## 493          10               50             1           1             1
## 494          10               50             0           0             0
## 495          10               50             0           0             1
## 496           1                5             0           0             0
## 497           9               45             0           0             0
## 498          10               50             0           0             0
## 499          10               50             0           0             0
## 500           7               35             0           0             1
## 501           0                0             1           1             0
## 502           0                0             1           1             0
## 503           0                0             1           1             0
## 504           0                0             1           1             0
## 505           0                0             1           1             0
## 506           0                0             0           0             0
## 507           0                0             0           0             0
## 508           0                0             0           0             0
## 509           0                0             1           0             0
## 510           0                0             1           1             0
## 511           0                0             1           0             0
## 512           0                0             0           0             0
## 513           0                0             1           1             0
## 514           0                0             1           0             0
## 515           0                0             1           1             0
## 516           0                0             1           0             0
## 517           0                0             0           0             0
## 518           0                0             1           0             0
## 519           0                0             1           1             0
## 520           0                0             1           0             0
## 521           0                0             1           1             0
## 522           0                0             1           1             0
## 523           0                0             1           1             0
## 524           0                0             1           1             0
## 525           0                0             0           0             0
## 526           0                0             1           1             0
## 527           0                0             1           1             0
## 528           0                0             0           0             0
## 529           0                0             1           0             0
## 530           0                0             1           1             0
## 531           0                0             1           0             0
## 532           0                0             0           0             0
## 533           0                0             0           0             0
## 534           0                0             1           1             0
## 535           0                0             0           0             0
## 536           0                0             0           0             0
## 537           0                0             0           0             0
## 538           0                0             1           1             0
## 539           0                0             0           0             0
## 540           0                0             0           0             0
## 541           1               50             1           0             0
## 542           2              100             0           0             0
## 543           2              100             1           0             2
## 544           1               50             0           0             0
## 545           1               50             1           1             0
## 546           0                0             0           0             2
## 547           2              100             1           1             0
## 548           1               50             1           1             0
## 549           0                0             1           1             0
## 550           1               50             1           0             0
## 551           1               50             1           1             0
## 552           2              100             1           0             0
## 553           2              100             0           0             0
## 554           2              100             1           0             0
## 555           0                0             1           1             0
## 556           2              100             1           1             0
## 557           1               50             1           1             0
## 558           2              100             1           1             0
## 559           2              100             1           1             0
## 560           2              100             1           0             0
## 561           2              100             1           1             0
## 562           2              100             1           1             0
## 563           2              100             0           0             0
## 564           2              100             0           0             0
## 565           1               50             0           0             0
## 566           2              100             1           1             0
## 567           2              100             0           0             0
## 568           2              100             0           0             0
## 569           1               50             1           1             0
## 570           0                0             0           0             0
## 571           0                0             1           0             0
## 572           1               50             0           0             0
## 573           1               50             1           1             0
## 574           2              100             1           1             0
## 575           2              100             1           0             0
## 576           2              100             0           0             0
## 577           2              100             1           1             0
## 578           2              100             0           0             0
## 579           1               50             0           0             0
## 580           2              100             1           1             0
## 581           4               80             1           1             0
## 582           0                0             1           1             0
## 583           5              100             1           1             0
## 584           3               60             1           1             0
## 585           3               60             1           1             0
## 586           4               80             0           0             0
## 587           0                0             0           0             0
## 588           5              100             0           0             3
## 589           5              100             0           0             0
## 590           3               60             0           0             0
## 591           5              100             1           1             0
## 592           2               40             0           0             0
## 593           5              100             0           0             0
## 594           3               60             0           0             0
## 595           2               40             0           0             0
## 596           1               20             1           1             0
## 597           5              100             1           1             0
## 598           2               40             1           0             2
## 599           5              100             0           0             1
## 600           5              100             0           0             0
## 601           4               80             0           0             0
## 602           5              100             0           0             0
## 603           5              100             0           0             0
## 604           5              100             0           0             1
## 605           4               80             1           1             0
## 606           5              100             1           1             0
## 607           3               60             0           0             0
## 608           5              100             0           0             0
## 609           3               60             0           0             0
## 610           4               80             0           0             0
## 611           5              100             0           0             2
## 612           3               60             0           0             0
## 613           4               80             0           0             1
## 614           3               60             0           0             0
## 615           4               80             1           0             0
## 616           2               40             0           0             0
## 617           5              100             1           1             0
## 618           3               60             1           1             0
## 619           3               60             1           1             0
## 620           0                0             1           1             0
## 621           2               20             0           0             0
## 622           6               60             1           0             0
## 623           6               60             0           0             0
## 624           6               60             1           1             0
## 625           6               60             0           0             0
## 626           5               50             0           0             0
## 627           7               70             1           1             0
## 628           5               50             0           0             0
## 629           8               80             1           1             0
## 630           6               60             0           0             0
## 631           8               80             1           0             0
## 632           5               50             1           1             0
## 633           5               50             0           0             0
## 634           6               60             0           0             0
## 635           9               90             0           0             3
## 636           6               60             0           0             0
## 637           1               10             1           1             0
## 638           4               40             1           0             2
## 639           5               50             1           0             0
## 640           5               50             0           0             0
## 641           7               70             1           1             0
## 642           4               40             1           1             0
## 643           7               70             1           0             0
## 644           7               70             0           0             0
## 645           8               80             1           1             0
## 646          10              100             0           0             0
## 647           8               80             1           1             0
## 648           5               50             1           1             0
## 649           6               60             0           0             0
## 650          10              100             0           0             0
## 651           7               70             0           0             0
## 652           4               40             0           0             0
## 653           7               70             1           1             0
## 654           6               60             1           1             0
## 655           3               30             0           0             0
## 656           7               70             1           1             0
## 657           7               70             0           0             0
## 658           4               40             1           1             1
## 659           7               70             0           0             1
## 660           7               70             0           0             0
## 661          12               60             1           0             0
## 662          13               65             1           1             0
## 663          13               65             1           1             0
## 664           8               40             1           1             0
## 665          15               75             1           1             0
## 666           5               25             1           0             0
## 667          13               65             1           0             1
## 668           7               35             1           1             0
## 669           8               40             0           0             0
## 670           7               35             1           0             0
## 671           6               30             0           0             0
## 672           1                5             1           1             0
## 673           8               40             1           0             0
## 674          13               65             0           0             0
## 675          11               55             1           0             0
## 676          11               55             0           0             0
## 677          10               50             1           1             0
## 678          13               65             0           0             4
## 679          11               55             0           0             0
## 680          12               60             0           0             0
## 681           7               35             0           0             0
## 682          10               50             1           1             0
## 683          15               75             0           0             0
## 684          14               70             1           1             0
## 685          10               50             1           1             1
## 686          15               75             1           0             1
## 687           8               40             0           0             0
## 688          13               65             0           0             0
## 689          13               65             1           0             0
## 690          12               60             1           0             0
## 691          10               50             0           0             0
## 692           7               35             0           0             0
## 693          12               60             1           1             2
## 694           8               40             0           0             0
## 695           9               45             0           0             0
## 696          13               65             0           0             1
## 697          11               55             1           0             0
## 698          13               65             1           1             2
## 699          14               70             0           0             0
## 700          10               50             1           1             0
##     Ephedra.above Ephedra.below Ephedra.biomass brome.biomass          test
## 1         0.00550       0.00120         0.00670       0.00000  clipped-once
## 2         0.02650       0.00350         0.03000       0.09180  clipped-once
## 3         0.01360       0.00510         0.01870       0.25030  clipped-once
## 4         0.00000       0.00000         0.00000       0.00000  clipped-once
## 5         0.02130       0.00530         0.02660       0.12160  clipped-once
## 6         0.00000       0.00000         0.00000       0.29580  clipped-once
## 7         0.00000       0.00000         0.00000       0.26070  clipped-once
## 8         0.01650       0.00820         0.02470       0.18090  clipped-once
## 9         0.00000       0.00000         0.00000       0.20730  clipped-once
## 10        0.00000       0.00000         0.00000       0.28800  clipped-once
## 11        0.00000       0.00000         0.00000       0.00000  clipped-once
## 12        0.03620       0.00600         0.04220       0.37190  clipped-once
## 13        0.00000       0.00000         0.00000       0.05550  clipped-once
## 14        0.00000       0.00000         0.00000       0.00000  clipped-once
## 15        0.00000       0.00000         0.00000       0.19680  clipped-once
## 16        0.00000       0.00000         0.00000       0.00000  clipped-once
## 17        0.02370       0.00460         0.02830       0.09410  clipped-once
## 18        0.00000       0.00000         0.00000       0.64990  clipped-once
## 19        0.00000       0.00000         0.00000       0.37030  clipped-once
## 20        0.00000       0.00000         0.00000       0.38870  clipped-once
## 21        0.00000       0.00000         0.00000       0.10390 clipped-twice
## 22        0.00000       0.00000         0.00000       0.12920 clipped-twice
## 23        0.01850       0.00000         0.01850       0.08190 clipped-twice
## 24        0.01300       0.00080         0.01380       0.00000 clipped-twice
## 25        0.00000       0.00000         0.00000       0.20410 clipped-twice
## 26        0.00000       0.00000         0.00000       0.12900 clipped-twice
## 27        0.00000       0.00000         0.00000       0.11510 clipped-twice
## 28        0.01280       0.00530         0.01810       0.07580 clipped-twice
## 29        0.00000       0.00000         0.00000       0.10430 clipped-twice
## 30        0.02450       0.00260         0.02710       0.30570 clipped-twice
## 31        0.03030       0.00830         0.03860       0.00000 clipped-twice
## 32        0.04260       0.00930         0.05190       0.22820 clipped-twice
## 33        0.00000       0.00000         0.00000       0.16880 clipped-twice
## 34        0.00930       0.00320         0.01250       0.00000 clipped-twice
## 35        0.00000       0.00000         0.00000       0.63810 clipped-twice
## 36        0.01810       0.00310         0.02120       0.00000 clipped-twice
## 37        0.01650       0.00270         0.01920       0.05580 clipped-twice
## 38        0.01550       0.00080         0.01630       0.25570 clipped-twice
## 39        0.00000       0.00000         0.00000       0.31530 clipped-twice
## 40        0.00000       0.00000         0.00000       0.43460 clipped-twice
## 41        0.01070       0.00080         0.01150       0.28450  clipped-once
## 42        0.00000       0.00000         0.00000       0.18080  clipped-once
## 43        0.00000       0.00000         0.00000       0.00000  clipped-once
## 44        0.00000       0.00000         0.00000       0.51090  clipped-once
## 45        0.00000       0.00000         0.00000       0.49770  clipped-once
## 46        0.00000       0.00000         0.00000       0.37290  clipped-once
## 47        0.00000       0.00000         0.00000       0.00000  clipped-once
## 48        0.02490       0.00640         0.03130       0.48910  clipped-once
## 49        0.00000       0.00000         0.00000       0.26980  clipped-once
## 50        0.03850       0.00740         0.04590       0.09020  clipped-once
## 51        0.00000       0.00000         0.00000       0.06860  clipped-once
## 52        0.00000       0.00000         0.00000       0.00000  clipped-once
## 53        0.00000       0.00000         0.00000       0.04360  clipped-once
## 54        0.00000       0.00000         0.00000       0.04860  clipped-once
## 55        0.00000       0.00000         0.00000       0.34990  clipped-once
## 56        0.00000       0.00000         0.00000       0.08430  clipped-once
## 57        0.00000       0.00000         0.00000       0.05540  clipped-once
## 58        0.01160       0.00350         0.01510       0.42220  clipped-once
## 59        0.05680       0.00790         0.06470       0.08060  clipped-once
## 60        0.00000       0.00000         0.00000       0.14490  clipped-once
## 61        0.04010       0.01200         0.05210       0.22380 clipped-twice
## 62        0.02610       0.01290         0.03900       0.07840 clipped-twice
## 63        0.00000       0.00000         0.00000       0.00000 clipped-twice
## 64        0.01410       0.00560         0.01970       0.10500 clipped-twice
## 65        0.01290       0.00410         0.01700       0.31520 clipped-twice
## 66        0.03570       0.00750         0.04320       0.13820 clipped-twice
## 67        0.00000       0.00000         0.00000       0.00000 clipped-twice
## 68        0.00000       0.00000         0.00000       0.08840 clipped-twice
## 69        0.00000       0.00000         0.00000       0.20450 clipped-twice
## 70        0.00900       0.00360         0.01260       0.05780 clipped-twice
## 71        0.00000       0.00000         0.00000       0.07440 clipped-twice
## 72        0.00900       0.00250         0.01150       0.32930 clipped-twice
## 73        0.00000       0.00000         0.00000       0.03150 clipped-twice
## 74        0.00990       0.00500         0.01490       0.00000 clipped-twice
## 75        0.00000       0.00000         0.00000       0.29070 clipped-twice
## 76        0.00000       0.00000         0.00000       0.06400 clipped-twice
## 77        0.00000       0.00000         0.00000       0.36160 clipped-twice
## 78        0.00000       0.00000         0.00000       0.08940 clipped-twice
## 79        0.02130       0.00510         0.02640       0.06920 clipped-twice
## 80        0.00000       0.00000         0.00000       0.14790 clipped-twice
## 81        0.00000       0.00000         0.00000       0.97380  clipped-once
## 82        0.00000       0.00000         0.00000       0.07510  clipped-once
## 83        0.00000       0.00000         0.00000       0.00000  clipped-once
## 84        0.02700       0.00230         0.02930       0.37440  clipped-once
## 85        0.00000       0.00000         0.00000       0.00000  clipped-once
## 86        0.03300       0.00550         0.03850       0.05470  clipped-once
## 87        0.00000       0.00000         0.00000       0.28710  clipped-once
## 88        0.00000       0.00000         0.00000       0.13070  clipped-once
## 89        0.00000       0.00000         0.00000       0.00000  clipped-once
## 90        0.00000       0.00000         0.00000       0.00000  clipped-once
## 91        0.04280       0.00770         0.05050       0.14800  clipped-once
## 92        0.00000       0.00000         0.00000       0.00000  clipped-once
## 93        0.00000       0.00000         0.00000       0.06470  clipped-once
## 94        0.00000       0.00000         0.00000       0.36080  clipped-once
## 95        0.00000       0.00000         0.00000       0.00000  clipped-once
## 96        0.00560       0.00270         0.00830       0.48060  clipped-once
## 97        0.00000       0.00000         0.00000       0.18510  clipped-once
## 98        0.00000       0.00000         0.00000       0.03410  clipped-once
## 99        0.00850       0.00180         0.01030       0.24800  clipped-once
## 100       0.01120       0.00560         0.01680       0.12510  clipped-once
## 101       0.00000       0.00000         0.00000       0.22280 clipped-twice
## 102       0.00000       0.00000         0.00000       0.27740 clipped-twice
## 103       0.00000       0.00000         0.00000       0.00000 clipped-twice
## 104       0.00000       0.00000         0.00000       0.16200 clipped-twice
## 105       0.01540       0.00220         0.01760       0.00000 clipped-twice
## 106       0.00000       0.00000         0.00000       0.13150 clipped-twice
## 107       0.01820       0.00520         0.02340       0.13440 clipped-twice
## 108       0.04970       0.01330         0.06300       0.19300 clipped-twice
## 109       0.01480       0.00230         0.01710       0.00000 clipped-twice
## 110       0.01200       0.00220         0.01420       0.04960 clipped-twice
## 111       0.00000       0.00000         0.00000       0.15610 clipped-twice
## 112       0.00000       0.00000         0.00000       0.49510 clipped-twice
## 113       0.00820       0.00220         0.01040       0.07590 clipped-twice
## 114       0.00000       0.00000         0.00000       0.55020 clipped-twice
## 115       0.00000       0.00000         0.00000       0.00000 clipped-twice
## 116       0.00000       0.00000         0.00000       0.74260 clipped-twice
## 117       0.00000       0.00000         0.00000       0.23590 clipped-twice
## 118       0.00000       0.00000         0.00000       0.06120 clipped-twice
## 119       0.00150       0.00160         0.00310       0.09730 clipped-twice
## 120       0.00000       0.00000         0.00000       0.07230 clipped-twice
## 121       0.02430       0.00680         0.03110       0.34550  clipped-once
## 122       0.00000       0.00000         0.00000       0.08370  clipped-once
## 123       0.00000       0.00000         0.00000       0.52100  clipped-once
## 124       0.02340       0.00480         0.02820       0.17470  clipped-once
## 125       0.00000       0.00000         0.00000       0.00000  clipped-once
## 126       0.00000       0.00000         0.00000       0.36200  clipped-once
## 127       0.00000       0.00000         0.00000       0.00000  clipped-once
## 128       0.00000       0.00000         0.00000       0.11290  clipped-once
## 129       0.02560       0.00530         0.03090       0.11980  clipped-once
## 130       0.01280       0.00260         0.01540       0.29680  clipped-once
## 131       0.00000       0.00000         0.00000       0.03630  clipped-once
## 132       0.01900       0.00490         0.02390       0.12700  clipped-once
## 133       0.02270       0.00920         0.03190       0.03560  clipped-once
## 134       0.04150       0.00480         0.04630       0.31550  clipped-once
## 135       0.00000       0.00000         0.00000       0.00000  clipped-once
## 136       0.00000       0.00000         0.00000       0.00000  clipped-once
## 137       0.00000       0.00000         0.00000       0.10080  clipped-once
## 138       0.00000       0.00000         0.00000       0.00000  clipped-once
## 139       0.00000       0.00000         0.00000       0.75300  clipped-once
## 140       0.00000       0.00000         0.00000       0.11050  clipped-once
## 141       0.00000       0.00000         0.00000       0.11840 clipped-twice
## 142       0.02530       0.00610         0.03140       0.07840 clipped-twice
## 143       0.00000       0.00000         0.00000       0.04040 clipped-twice
## 144       0.00000       0.00000         0.00000       0.21310 clipped-twice
## 145       0.00820       0.00490         0.01310       0.00000 clipped-twice
## 146       0.00300       0.00060         0.00360       0.20720 clipped-twice
## 147       0.00000       0.00000         0.00000       0.11400 clipped-twice
## 148       0.00000       0.00000         0.00000       0.06970 clipped-twice
## 149       0.00000       0.00000         0.00000       0.08230 clipped-twice
## 150       0.00000       0.00000         0.00000       0.26620 clipped-twice
## 151       0.00000       0.00000         0.00000       0.05840 clipped-twice
## 152       0.00000       0.00000         0.00000       0.04610 clipped-twice
## 153       0.00000       0.00000         0.00000       0.09150 clipped-twice
## 154       0.00000       0.00000         0.00000       0.50060 clipped-twice
## 155       0.00000       0.00000         0.00000       0.00000 clipped-twice
## 156       0.00000       0.00000         0.00000       0.00000 clipped-twice
## 157       0.00000       0.00000         0.00000       0.11740 clipped-twice
## 158       0.01170       0.00270         0.01440       0.00000 clipped-twice
## 159       0.00000       0.00000         0.00000       0.40220 clipped-twice
## 160       0.01240       0.00200         0.01440       0.05850 clipped-twice
## 161       0.00000       0.00000         0.00000       0.75040  clipped-once
## 162       0.06560       0.01170         0.07730       0.00000  clipped-once
## 163       0.00000       0.00000         0.00000       0.00000  clipped-once
## 164       0.03600       0.00780         0.04380       0.13120  clipped-once
## 165       0.00000       0.00000         0.00000       0.33800  clipped-once
## 166       0.01150       0.00230         0.01380       0.12240  clipped-once
## 167       0.00000       0.00000         0.00000       0.22720  clipped-once
## 168       0.00000       0.00000         0.00000       0.18500  clipped-once
## 169       0.03550       0.00100         0.03650       0.14660  clipped-once
## 170       0.01950       0.00380         0.02330       0.29450  clipped-once
## 171       0.00810       0.00500         0.01310       0.40970  clipped-once
## 172       0.01220       0.00430         0.01650       0.00000  clipped-once
## 173       0.00000       0.00000         0.00000       0.35110  clipped-once
## 174       0.00000       0.00000         0.00000       0.59720  clipped-once
## 175       0.00000       0.00000         0.00000       0.00000  clipped-once
## 176       0.00000       0.00000         0.00000       0.00000  clipped-once
## 177       0.00000       0.00000         0.00000       0.20830  clipped-once
## 178       0.00000       0.00000         0.00000       0.00000  clipped-once
## 179       0.00000       0.00000         0.00000       0.00000  clipped-once
## 180       0.00000       0.00000         0.00000       0.14880  clipped-once
## 181       0.00770       0.00000         0.00770       0.16940 clipped-twice
## 182       0.01310       0.00270         0.01580       0.00000 clipped-twice
## 183       0.00000       0.00000         0.00000       0.00000 clipped-twice
## 184       0.00000       0.00000         0.00000       0.08240 clipped-twice
## 185       0.00000       0.00000         0.00000       0.22150 clipped-twice
## 186       0.00720       0.00080         0.00800       0.08980 clipped-twice
## 187       0.00000       0.00000         0.00000       0.05690 clipped-twice
## 188       0.00000       0.00000         0.00000       0.05500 clipped-twice
## 189       0.00000       0.00000         0.00000       0.63270 clipped-twice
## 190       0.00000       0.00000         0.00000       0.30780 clipped-twice
## 191       0.03100       0.00870         0.03970       0.23010 clipped-twice
## 192       0.01410       0.00130         0.01540       0.00000 clipped-twice
## 193       0.01750       0.00130         0.01880       0.46290 clipped-twice
## 194       0.01240       0.00260         0.01500       0.21450 clipped-twice
## 195       0.00000       0.00000         0.00000       0.00000 clipped-twice
## 196       0.00000       0.00000         0.00000       0.00000 clipped-twice
## 197       0.00000       0.00000         0.00000       0.52390 clipped-twice
## 198       0.00000       0.00000         0.00000       0.00000 clipped-twice
## 199       0.00000       0.00000         0.00000       0.05120 clipped-twice
## 200       0.01320       0.00140         0.01460       0.00000 clipped-twice
## 201       0.00000       0.00000         0.00000       0.26740  control-none
## 202       0.01110       0.00190         0.01300       0.15880  control-none
## 203       0.03880       0.00270         0.04150       0.10360  control-none
## 204       0.00000       0.00000         0.00000       0.00000  control-none
## 205       0.00000       0.00000         0.00000       0.00000  control-none
## 206       0.03070       0.00230         0.03300       0.12130  control-none
## 207       0.00000       0.00000         0.00000       0.19280  control-none
## 208       0.00000       0.00000         0.00000       0.17980  control-none
## 209       0.06990       0.01180         0.07180       0.79270  control-none
## 210       0.03840       0.00690         0.04530       0.58480  control-none
## 211       0.00000       0.00000         0.00000       0.00000  control-none
## 212       0.00000       0.00000         0.00000       0.54080  control-none
## 213       0.00000       0.00000         0.00000       0.28460  control-none
## 214       0.04600       0.00760         0.05360       0.00000  control-none
## 215       0.00000       0.00000         0.00000       0.64600  control-none
## 216       0.02830       0.00550         0.03380       0.00000  control-none
## 217       0.00000       0.00000         0.00000       0.18060  control-none
## 218       0.00000       0.00000         0.00000       0.51500  control-none
## 219       0.00000       0.00000         0.00000       0.47590  control-none
## 220       0.00000       0.00000         0.00000       0.62080  control-none
## 221       0.01240       0.00530         0.01770       0.33220  control-none
## 222       0.08860       0.01020         0.09880       0.24710  control-none
## 223       0.00000       0.00000         0.00000       0.23960  control-none
## 224       0.00350       0.00000         0.00350       0.47170  control-none
## 225       0.04330       0.00440         0.04770       0.26980  control-none
## 226       0.03900       0.00650         0.04550       0.44520  control-none
## 227       0.00000       0.00000         0.00000       0.07190  control-none
## 228       0.00000       0.00000         0.00000       0.25540  control-none
## 229       0.00000       0.00000         0.00000       0.56060  control-none
## 230       0.05980       0.00940         0.06920       0.48800  control-none
## 231       0.03560       0.00410         0.03970       0.01880  control-none
## 232       0.05700       0.01200         0.06900       0.70010  control-none
## 233       0.00000       0.00000         0.00000       0.09610  control-none
## 234       0.00000       0.00000         0.00000       0.08420  control-none
## 235       0.00000       0.00000         0.00000       0.19430  control-none
## 236       0.05690       0.01030         0.06720       0.16430  control-none
## 237       0.00000       0.00000         0.00000       0.10320  control-none
## 238       0.03300       0.00790         0.04090       0.25460  control-none
## 239       0.00000       0.00000         0.00000       0.15270  control-none
## 240       0.02760       0.00770         0.03530       0.19710  control-none
## 241       0.00000       0.00000         0.00000       0.40440  control-none
## 242       0.06080       0.01290         0.07370       0.34680  control-none
## 243       0.00000       0.00000         0.00000       0.00000  control-none
## 244       0.01850       0.00410         0.02260       0.12600  control-none
## 245       0.03220       0.00850         0.04070       0.00000  control-none
## 246       0.00000       0.00000         0.00000       0.72250  control-none
## 247       0.00000       0.00000         0.00000       0.58350  control-none
## 248       0.01660       0.00140         0.01800       0.22040  control-none
## 249       0.03030       0.00380         0.03410       0.00000  control-none
## 250       0.03990       0.00470         0.04460       0.00000  control-none
## 251       0.00000       0.00000         0.00000       0.21270  control-none
## 252       0.00000       0.00000         0.00000       0.14510  control-none
## 253       0.00000       0.00000         0.00000       0.07130  control-none
## 254       0.00000       0.00000         0.00000       0.55520  control-none
## 255       0.00000       0.00000         0.00000       0.00000  control-none
## 256       0.00000       0.00000         0.00000       0.58590  control-none
## 257       0.00000       0.00000         0.00000       0.20620  control-none
## 258       0.00000       0.00000         0.00000       0.21800  control-none
## 259       0.00000       0.00000         0.00000       0.13050  control-none
## 260       0.00000       0.00000         0.00000       0.21200  control-none
## 261       0.00000       0.00000         0.00000       0.39010  control-none
## 262       0.01580       0.00400         0.01980       0.18070  control-none
## 263       0.00000       0.00000         0.00000       0.08230  control-none
## 264       0.04550       0.00490         0.05040       0.31070  control-none
## 265       0.06410       0.01890         0.08300       0.00000  control-none
## 266       0.00000       0.00000         0.00000       0.61500  control-none
## 267       0.00000       0.00000         0.00000       0.00000  control-none
## 268       0.00000       0.00000         0.00000       0.07120  control-none
## 269       0.03720       0.00550         0.04270       0.32410  control-none
## 270       0.06100       0.01660         0.07760       0.21200  control-none
## 271       0.00000       0.00000         0.00000       0.09400  control-none
## 272       0.00000       0.00000         0.00000       0.16790  control-none
## 273       0.06320       0.00790         0.07110       0.15580  control-none
## 274       0.00000       0.00000         0.00000       0.33890  control-none
## 275       0.00000       0.00000         0.00000       0.00000  control-none
## 276       0.00000       0.00000         0.00000       0.00000  control-none
## 277       0.00920       0.00210         0.01130       0.13280  control-none
## 278       0.00000       0.00000         0.00000       0.00000  control-none
## 279       0.00000       0.00000         0.00000       0.23810  control-none
## 280       0.02680       0.00730         0.03410       0.07970  control-none
## 281       0.00000       0.00000         0.00000       0.40410  control-none
## 282       0.00000       0.00000         0.00000       0.00000  control-none
## 283       0.00000       0.00000         0.00000       0.00000  control-none
## 284       0.00000       0.00000         0.00000       0.53350  control-none
## 285       0.00000       0.00000         0.00000       0.64980  control-none
## 286       0.03330       0.00000         0.03330       0.43210  control-none
## 287       0.00000       0.00610         0.00610       0.11750  control-none
## 288       0.00000       0.00000         0.00000       0.18620  control-none
## 289       0.04940       0.01460         0.06400       0.63010  control-none
## 290       0.00000       0.00000         0.00000       0.42480  control-none
## 291       0.00000       0.00000         0.00000       0.19640  control-none
## 292       0.00000       0.00000         0.00000       0.00000  control-none
## 293       0.00000       0.00000         0.00000       0.40760  control-none
## 294       0.01220       0.00270         0.01490       0.24880  control-none
## 295       0.00000       0.00000         0.00000       0.00000  control-none
## 296       0.00000       0.00000         0.00000       0.00000  control-none
## 297       0.00000       0.00000         0.00000       0.35760  control-none
## 298       0.00000       0.00000         0.00000       0.00000  control-none
## 299       0.00000       0.00000         0.00000       0.17540  control-none
## 300       0.00000       0.00000         0.00000       0.26390  control-none
## 301       0.03520       0.00490         0.04010       0.13690    shade-high
## 302       0.00000       0.00000         0.00000       0.11630    shade-high
## 303       0.00000       0.00000         0.00000       0.13920    shade-high
## 304       0.00000       0.00000         0.00000       0.00000    shade-high
## 305       0.00000       0.00000         0.00000       0.10280    shade-high
## 306       0.03260       0.00080         0.03340       0.03700    shade-high
## 307       0.00000       0.00000         0.00000       0.13280    shade-high
## 308       0.00000       0.00000         0.00000       0.09610    shade-high
## 309       0.00000       0.00000         0.00000       0.28290    shade-high
## 310       0.00000       0.00000         0.00000       0.00000    shade-high
## 311       0.00000       0.00000         0.00000       0.00000    shade-high
## 312       0.00000       0.00000         0.00000       0.22240    shade-high
## 313       0.02280       0.00570         0.02850       0.23670    shade-high
## 314       0.00000       0.00000         0.00000       0.00000    shade-high
## 315       0.00000       0.00000         0.00000       0.25500    shade-high
## 316       0.02230       0.00270         0.02500       0.00000    shade-high
## 317       0.00000       0.00000         0.00000       0.07660    shade-high
## 318       0.00000       0.00000         0.00000       0.23500    shade-high
## 319       0.00000       0.00000         0.00000       0.13050    shade-high
## 320       0.00000       0.00000         0.00000       0.00000    shade-high
## 321       0.00000       0.00000         0.00000       0.16580     shade-med
## 322       0.00000       0.00000         0.00000       0.20550     shade-med
## 323       0.00000       0.00000         0.00000       0.31370     shade-med
## 324       0.05320       0.00620         0.05940       0.00000     shade-med
## 325       0.01200       0.00130         0.01330       0.22010     shade-med
## 326       0.00000       0.00000         0.00000       0.30350     shade-med
## 327       0.00000       0.00000         0.00000       0.36030     shade-med
## 328       0.00000       0.00000         0.00000       0.14580     shade-med
## 329       0.00000       0.00000         0.00000       0.20870     shade-med
## 330       0.00000       0.00000         0.00000       0.23930     shade-med
## 331       0.00000       0.00000         0.00000       0.00000     shade-med
## 332       0.00000       0.00000         0.00000       0.32050     shade-med
## 333       0.00000       0.00000         0.00000       0.18900     shade-med
## 334       0.00000       0.00000         0.00000       0.00000     shade-med
## 335       0.00000       0.00000         0.00000       0.14870     shade-med
## 336       0.00000       0.00000         0.00000       0.00000     shade-med
## 337       0.00000       0.00000         0.00000       0.09670     shade-med
## 338       0.00000       0.00000         0.00000       0.56820     shade-med
## 339       0.00000       0.00000         0.00000       0.22460     shade-med
## 340       0.00000       0.00000         0.00000       0.86120     shade-med
## 341       0.00000       0.00000         0.00000       0.24180    shade-high
## 342       0.02870       0.00230         0.03100       0.15810    shade-high
## 343       0.00000       0.00000         0.00000       0.00000    shade-high
## 344       0.00000       0.00000         0.00000       0.28430    shade-high
## 345       0.00000       0.00000         0.00000       0.35110    shade-high
## 346       0.00000       0.00000         0.00000       1.11320    shade-high
## 347       0.00000       0.00000         0.00000       0.01380    shade-high
## 348       0.00000       0.00000         0.00000       0.09180    shade-high
## 349       0.01830       0.00280         0.02110       0.09270    shade-high
## 350       0.00550       0.00040         0.00590       0.03290    shade-high
## 351       0.00000       0.00000         0.00000       0.03820    shade-high
## 352       0.00000       0.00000         0.00000       0.13830    shade-high
## 353       0.00000       0.00000         0.00000       0.08510    shade-high
## 354       0.00000       0.00000         0.00000       0.04030    shade-high
## 355       0.00000       0.00000         0.00000       0.18130    shade-high
## 356       0.00000       0.00000         0.00000       0.04520    shade-high
## 357       0.00000       0.00000         0.00000       0.08300    shade-high
## 358       0.00000       0.00000         0.00000       0.04690    shade-high
## 359       0.00000       0.00000         0.00000       0.04090    shade-high
## 360       0.00000       0.00000         0.00000       0.08500    shade-high
## 361       0.00000       0.00000         0.00000       0.28350     shade-med
## 362       0.07030       0.00830         0.07860       0.27440     shade-med
## 363       0.00000       0.00000         0.00000       0.00000     shade-med
## 364       0.00000       0.00000         0.00000       0.72950     shade-med
## 365       0.00000       0.00000         0.00000       0.73950     shade-med
## 366       0.00000       0.00000         0.00000       0.52640     shade-med
## 367       0.00000       0.00000         0.00000       0.00000     shade-med
## 368       0.00000       0.00000         0.00000       0.58350     shade-med
## 369       0.00000       0.00000         0.00000       0.37550     shade-med
## 370       0.03490       0.00670         0.04160       0.14020     shade-med
## 371       0.00000       0.00000         0.00000       0.21470     shade-med
## 372       0.00000       0.00000         0.00000       0.59210     shade-med
## 373       0.00000       0.00000         0.00000       0.00000     shade-med
## 374       0.00000       0.00000         0.00000       0.02350     shade-med
## 375       0.00000       0.00000         0.00000       0.48560     shade-med
## 376       0.00000       0.00000         0.00000       0.11270     shade-med
## 377       0.00000       0.00000         0.00000       0.42410     shade-med
## 378       0.00000       0.00000         0.00000       0.19010     shade-med
## 379       0.00000       0.00000         0.00000       0.20510     shade-med
## 380       0.00000       0.00000         0.00000       0.62410     shade-med
## 381       0.03240       0.00360         0.03600       0.71650    shade-high
## 382       0.00000       0.00000         0.00000       0.40280    shade-high
## 383       0.00000       0.00000         0.00000       0.00000    shade-high
## 384       0.00000       0.00000         0.00000       0.27550    shade-high
## 385       0.00000       0.00000         0.00000       0.00000    shade-high
## 386       0.00000       0.00000         0.00000       0.10940    shade-high
## 387       0.00000       0.00000         0.00000       0.21560    shade-high
## 388       0.00000       0.00000         0.00000       0.12820    shade-high
## 389       0.01680       0.00450         0.02130       0.00000    shade-high
## 390       0.00000       0.00000         0.00000       0.00000    shade-high
## 391       0.00000       0.00000         0.00000       0.11340    shade-high
## 392       0.00000       0.00000         0.00000       0.00000    shade-high
## 393       0.03810       0.00260         0.04070       0.06780    shade-high
## 394       0.00000       0.00000         0.00000       0.30480    shade-high
## 395       0.02720       0.00320         0.03040       0.00000    shade-high
## 396       0.00000       0.00000         0.00000       0.14127    shade-high
## 397       0.00000       0.00000         0.00000       0.01650    shade-high
## 398       0.00000       0.00000         0.00000       0.02260    shade-high
## 399       0.00000       0.00000         0.00000       0.16820    shade-high
## 400       0.03010       0.00090         0.03100       0.03500    shade-high
## 401       0.00000       0.00000         0.00000       0.15950     shade-med
## 402       0.00000       0.00000         0.00000       0.54120     shade-med
## 403       0.00000       0.00000         0.00000       0.00000     shade-med
## 404       0.00000       0.00000         0.00000       0.57490     shade-med
## 405       0.00000       0.00000         0.00000       0.00000     shade-med
## 406       0.00000       0.00000         0.00000       0.15560     shade-med
## 407       0.00000       0.00000         0.00000       0.25330     shade-med
## 408       0.01210       0.00140         0.01350       0.32090     shade-med
## 409       0.00000       0.00000         0.00000       0.00000     shade-med
## 410       0.00000       0.00000         0.00000       0.00000     shade-med
## 411       0.00000       0.00000         0.00000       0.07500     shade-med
## 412       0.00000       0.00000         0.00000       0.39750     shade-med
## 413       0.00000       0.00000         0.00000       0.13500     shade-med
## 414       0.00000       0.00000         0.00000       0.97110     shade-med
## 415       0.00000       0.00000         0.00000       0.00000     shade-med
## 416       0.00000       0.00000         0.00000       0.44120     shade-med
## 417       0.00000       0.00000         0.00000       0.38860     shade-med
## 418       0.00000       0.00000         0.00000       0.08530     shade-med
## 419       0.06190       0.00430         0.06620       0.09690     shade-med
## 420       0.00000       0.00000         0.00000       0.03760     shade-med
## 421       0.03220       0.00900         0.04120       0.16740    shade-high
## 422       0.00000       0.00000         0.00000       0.05730    shade-high
## 423       0.00000       0.00000         0.00000       0.12560    shade-high
## 424       0.00000       0.00000         0.00000       0.23380    shade-high
## 425       0.00000       0.00000         0.00000       0.02970    shade-high
## 426       0.00000       0.00000         0.00000       0.62390    shade-high
## 427       0.00000       0.00000         0.00000       0.06630    shade-high
## 428       0.00000       0.00000         0.00000       0.00000    shade-high
## 429       0.00000       0.00000         0.00000       0.09820    shade-high
## 430       0.00000       0.00000         0.00000       0.26320    shade-high
## 431       0.00000       0.00000         0.00000       0.02860    shade-high
## 432       0.00000       0.00000         0.00000       0.13500    shade-high
## 433       0.00000       0.00000         0.00000       0.07830    shade-high
## 434       0.00000       0.00000         0.00000       0.16210    shade-high
## 435       0.00000       0.00000         0.00000       0.00000    shade-high
## 436       0.00000       0.00000         0.00000       0.00000    shade-high
## 437       0.00000       0.00000         0.00000       0.00000    shade-high
## 438       0.00000       0.00000         0.00000       0.00000    shade-high
## 439       0.00000       0.00000         0.00000       0.23260    shade-high
## 440       0.00000       0.00000         0.00000       0.09420    shade-high
## 441       0.02680       0.01160         0.03840       0.24500     shade-med
## 442       0.00000       0.00000         0.00000       0.19780     shade-med
## 443       0.00000       0.00000         0.00000       0.15270     shade-med
## 444       0.00000       0.00000         0.00000       0.45260     shade-med
## 445       0.00000       0.00000         0.00000       0.00000     shade-med
## 446       0.00000       0.00000         0.00000       0.35680     shade-med
## 447       0.00000       0.00000         0.00000       0.00000     shade-med
## 448       0.02670       0.00160         0.02830       0.08550     shade-med
## 449       0.00000       0.00000         0.00000       0.15620     shade-med
## 450       0.00000       0.00000         0.00000       0.27920     shade-med
## 451       0.02160       0.00660         0.02820       0.16840     shade-med
## 452       0.00000       0.00000         0.00000       0.49780     shade-med
## 453       0.00000       0.00000         0.00000       0.22620     shade-med
## 454       0.00000       0.00000         0.00000       0.20090     shade-med
## 455       0.00000       0.00000         0.00000       0.00000     shade-med
## 456       0.00000       0.00000         0.00000       0.00000     shade-med
## 457       0.02930       0.00660         0.03590       0.14020     shade-med
## 458       0.02620       0.00370         0.02990       0.00000     shade-med
## 459       0.00000       0.00000         0.00000       0.47020     shade-med
## 460       0.00000       0.00000         0.00000       0.23670     shade-med
## 461       0.01340       0.00180         0.01520       0.60500    shade-high
## 462       0.00000       0.00000         0.00000       0.00000    shade-high
## 463       0.04330       0.00300         0.04630       0.00000    shade-high
## 464       0.00000       0.00000         0.00000       0.14650    shade-high
## 465       0.00000       0.00000         0.00000       0.32680    shade-high
## 466       0.02660       0.00420         0.03080       0.10670    shade-high
## 467       0.00910       0.00190         0.01100       0.07940    shade-high
## 468       0.00000       0.00000         0.00000       0.13500    shade-high
## 469       0.00000       0.00000         0.00000       0.10830    shade-high
## 470       0.00000       0.00000         0.00000       0.12260    shade-high
## 471       0.01810       0.00130         0.01940       0.17840    shade-high
## 472       0.00000       0.00000         0.00000       0.10020    shade-high
## 473       0.00000       0.00000         0.00000       0.40660    shade-high
## 474       0.00000       0.00000         0.00000       0.09090    shade-high
## 475       0.00000       0.00000         0.00000       0.00000    shade-high
## 476       0.00000       0.00000         0.00000       0.00000    shade-high
## 477       0.00000       0.00000         0.00000       0.14550    shade-high
## 478       0.00000       0.00000         0.00000       0.00000    shade-high
## 479       0.00000       0.00000         0.00000       0.06810    shade-high
## 480       0.00000       0.00000         0.00000       0.00000    shade-high
## 481       0.00000       0.00000         0.00000       0.31500     shade-med
## 482       0.00000       0.00000         0.00000       0.00000     shade-med
## 483       0.00000       0.00000         0.00000       0.00000     shade-med
## 484       0.00000       0.00000         0.00000       0.27620     shade-med
## 485       0.00000       0.00000         0.00000       0.86750     shade-med
## 486       0.00000       0.00000         0.00000       0.15160     shade-med
## 487       0.00000       0.00000         0.00000       0.14930     shade-med
## 488       0.00000       0.00000         0.00000       0.05990     shade-med
## 489       0.00000       0.00000         0.00000       0.24720     shade-med
## 490       0.00580       0.00290         0.00870       0.66190     shade-med
## 491       0.00000       0.00000         0.00000       0.08700     shade-med
## 492       0.00000       0.00000         0.00000       0.00000     shade-med
## 493       0.00000       0.00000         0.00000       0.37210     shade-med
## 494       0.00000       0.00000         0.00000       0.46990     shade-med
## 495       0.00000       0.00000         0.00000       0.00000     shade-med
## 496       0.03770       0.00560         0.04330       0.00000     shade-med
## 497       0.00000       0.00000         0.00000       0.55170     shade-med
## 498       0.00000       0.00000         0.00000       0.00000     shade-med
## 499       0.06350       0.01650         0.08000       0.00000     shade-med
## 500       0.00000       0.00000         0.00000       0.42340     shade-med
## 501       0.03100       0.00510         0.03610       0.40080    water-high
## 502       0.00000       0.00000         0.00000       0.75670    water-high
## 503       0.00000       0.00000         0.00000       0.67150    water-high
## 504       0.03980       0.00500         0.04480       0.00000    water-high
## 505       0.00000       0.00000         0.00000       0.00000    water-high
## 506       0.01140       0.00120         0.01260       0.17340    water-high
## 507       0.02990       0.00720         0.03710       1.47650    water-high
## 508       0.04280       0.00660         0.04940       0.00000    water-high
## 509       0.00000       0.00000         0.00000       0.65230    water-high
## 510       0.03820       0.00470         0.04290       2.21290    water-high
## 511       0.00000       0.00000         0.00000       0.00000    water-high
## 512       0.00000       0.00000         0.00000       1.98050    water-high
## 513       0.00800       0.00000         0.00800       1.10640    water-high
## 514       0.05280       0.01170         0.06450       0.00000    water-high
## 515       0.00000       0.00000         0.00000       1.47190    water-high
## 516       0.05730       0.01580         0.07310       0.00000    water-high
## 517       0.05860       0.01120         0.06980       1.27780    water-high
## 518       0.00000       0.00000         0.00000       0.00000    water-high
## 519       0.00000       0.00000         0.00000       0.79800    water-high
## 520       0.00000       0.00000         0.00000       1.53660    water-high
## 521       0.00000       0.00000         0.00000       1.58920     water-low
## 522       0.01460       0.00180         0.01640       0.12930     water-low
## 523       0.00000       0.00000         0.00000       0.59390     water-low
## 524       0.02780       0.00640         0.03420       0.00000     water-low
## 525       0.00000       0.00000         0.00000       0.35320     water-low
## 526       0.00000       0.00000         0.00000       0.43340     water-low
## 527       0.00000       0.00000         0.00000       0.83420     water-low
## 528       0.00000       0.00000         0.00000       0.56180     water-low
## 529       0.00000       0.00000         0.00000       0.95550     water-low
## 530       0.01380       0.00290         0.01670       1.82680     water-low
## 531       0.00000       0.00000         0.00000       0.00000     water-low
## 532       0.07780       0.00800         0.08580       0.00000     water-low
## 533       0.00000       0.00000         0.00000       1.78700     water-low
## 534       0.02060       0.00460         0.02520       0.00000     water-low
## 535       0.00000       0.00000         0.00000       1.77900     water-low
## 536       0.00000       0.00000         0.00000       0.00000     water-low
## 537       0.00000       0.00000         0.00000       0.62810     water-low
## 538       0.00000       0.00000         0.00000       1.32370     water-low
## 539       0.05920       0.01120         0.07040       0.67900     water-low
## 540       0.00000       0.00000         0.00000       1.20680     water-low
## 541       0.00000       0.00000         0.00000       0.59440    water-high
## 542       0.00000       0.00000         0.00000       0.62600    water-high
## 543       0.00000       0.00000         0.00000       0.00000    water-high
## 544       0.02640       0.00470         0.03110       1.97150    water-high
## 545       0.01040       0.00170         0.01210       2.69650    water-high
## 546       0.02750       0.00410         0.03160       3.51890    water-high
## 547       0.00000       0.00000         0.00000       0.76370    water-high
## 548       0.00000       0.00000         0.00000       1.24970    water-high
## 549       0.04420       0.01040         0.05460       1.56030    water-high
## 550       0.00000       0.00000         0.00000       0.71700    water-high
## 551       0.00190       0.00160         0.00350       0.43900    water-high
## 552       0.00000       0.00000         0.00000       1.30790    water-high
## 553       0.05450       0.00520         0.05970       0.43160    water-high
## 554       0.00000       0.00000         0.00000       0.57820    water-high
## 555       0.03570       0.01080         0.04650       0.56500    water-high
## 556       0.00000       0.00000         0.00000       0.86740    water-high
## 557       0.00000       0.00000         0.00000       1.21300    water-high
## 558       0.00000       0.00000         0.00000       0.31220    water-high
## 559       0.07600       0.01040         0.08640       0.36080    water-high
## 560       0.00000       0.00000         0.00000       0.23680    water-high
## 561       0.03090       0.00820         0.03910       0.66100     water-low
## 562       0.00000       0.00000         0.00000       0.79290     water-low
## 563       0.00000       0.00000         0.00000       0.00000     water-low
## 564       0.00000       0.00000         0.00000       0.43580     water-low
## 565       0.00000       0.00000         0.00000       0.50580     water-low
## 566       0.00000       0.00000         0.00000       1.88470     water-low
## 567       0.03820       0.00720         0.04540       0.09400     water-low
## 568       0.00000       0.00000         0.00000       1.58130     water-low
## 569       0.00000       0.00000         0.00000       0.31140     water-low
## 570       0.00000       0.00000         0.00000       0.63910     water-low
## 571       0.00000       0.00000         0.00000       0.34870     water-low
## 572       0.00000       0.00000         0.00000       2.07340     water-low
## 573       0.04080       0.00470         0.04550       0.10910     water-low
## 574       0.04210       0.00700         0.04910       0.19380     water-low
## 575       0.00000       0.00000         0.00000       0.45160     water-low
## 576       0.04720       0.00840         0.05560       0.28540     water-low
## 577       0.00000       0.00000         0.00000       1.08290     water-low
## 578       0.01440       0.00350         0.01790       0.73870     water-low
## 579       0.00000       0.00000         0.00000       0.28350     water-low
## 580       0.00000       0.00000         0.00000       0.70130     water-low
## 581       0.00000       0.00000         0.00000       1.03630    water-high
## 582       0.04300       0.00930         0.05230       0.37020    water-high
## 583       0.00000       0.00000         0.00000       0.00000    water-high
## 584       0.00000       0.00000         0.00000       0.65670    water-high
## 585       0.00880       0.00090         0.00970       0.00000    water-high
## 586       0.02460       0.00330         0.02790       0.75260    water-high
## 587       0.01580       0.00540         0.02120       1.71170    water-high
## 588       0.00000       0.00000         0.00000       1.48570    water-high
## 589       0.04780       0.00630         0.05410       0.00000    water-high
## 590       0.00000       0.00000         0.00000       0.00000    water-high
## 591       0.00000       0.00000         0.00000       0.36170    water-high
## 592       0.00000       0.00000         0.00000       2.13290    water-high
## 593       0.00000       0.00000         0.00000       0.66780    water-high
## 594       0.02510       0.00460         0.02970       3.02780    water-high
## 595       0.01290       0.00640         0.01930       0.00000    water-high
## 596       0.00000       0.00000         0.00000       1.79770    water-high
## 597       0.00000       0.00000         0.00000       2.72430    water-high
## 598       0.00000       0.00000         0.00000       1.47240    water-high
## 599       0.00000       0.00000         0.00000       0.13030    water-high
## 600       0.00000       0.00000         0.00000       0.05780    water-high
## 601       0.03950       0.00840         0.04790       0.71150     water-low
## 602       0.01990       0.00290         0.02280       0.71100     water-low
## 603       0.00000       0.00000         0.00000       0.00000     water-low
## 604       0.00000       0.00000         0.00000       0.96310     water-low
## 605       0.04240       0.00850         0.05090       0.00000     water-low
## 606       0.00000       0.00000         0.00000       0.11960     water-low
## 607       0.00000       0.00000         0.00000       1.13270     water-low
## 608       0.00000       0.00000         0.00000       0.62850     water-low
## 609       0.04270       0.01200         0.05470       0.00000     water-low
## 610       0.00000       0.00000         0.00000       0.81020     water-low
## 611       0.00000       0.00000         0.00000       0.14460     water-low
## 612       0.00000       0.00000         0.00000       0.00000     water-low
## 613       0.04710       0.01050         0.05760       0.04700     water-low
## 614       0.00000       0.00000         0.00000       2.47650     water-low
## 615       0.00000       0.00000         0.00000       0.00000     water-low
## 616       0.00000       0.00000         0.00000       3.03630     water-low
## 617       0.03960       0.00000         0.03960       0.69670     water-low
## 618       0.00000       0.00000         0.00000       0.29100     water-low
## 619       0.00000       0.00000         0.00000       0.00000     water-low
## 620       0.00000       0.00000         0.00000       0.28710     water-low
## 621       0.00000       0.00000         0.00000       0.16570    water-high
## 622       0.01620       0.00170         0.01790       0.18540    water-high
## 623       0.00000       0.00000         0.00000       0.50660    water-high
## 624       0.00000       0.00000         0.00000       1.86340    water-high
## 625       0.00000       0.00000         0.00000       0.00000    water-high
## 626       0.00000       0.00000         0.00000       3.29120    water-high
## 627       0.04830       0.00680         0.05510       1.03610    water-high
## 628       0.03290       0.01400         0.04690       0.00000    water-high
## 629       0.00000       0.00000         0.00000       1.07190    water-high
## 630       0.07340       0.01560         0.08900       3.15560    water-high
## 631       0.00000       0.00000         0.00000       0.00000    water-high
## 632       0.00000       0.00000         0.00000       1.08420    water-high
## 633       0.00000       0.00000         0.00000       1.55460    water-high
## 634       0.00000       0.00000         0.00000       1.55010    water-high
## 635       0.04960       0.01200         0.06160       0.00000    water-high
## 636       0.00000       0.00000         0.00000       0.00000    water-high
## 637       0.00000       0.00000         0.00000       0.77010    water-high
## 638       0.00000       0.00000         0.00000       0.00000    water-high
## 639       0.00000       0.00000         0.00000       1.85760    water-high
## 640       0.00000       0.00000         0.00000       0.13240    water-high
## 641       0.02110       0.00410         0.02520       0.22330     water-low
## 642       0.00000       0.00000         0.00000       1.50170     water-low
## 643       0.02830       0.00530         0.03360       0.69590     water-low
## 644       0.06650       0.01300         0.07950       1.20800     water-low
## 645       0.00000       0.00000         0.00000       0.00000     water-low
## 646       0.00000       0.00000         0.00000       0.97640     water-low
## 647       0.00000       0.00000         0.00000       0.30640     water-low
## 648       0.00434       0.00300         0.00734       0.10810     water-low
## 649       0.00000       0.00000         0.00000       0.50970     water-low
## 650       0.03110       0.00510         0.03620       1.40070     water-low
## 651       0.02830       0.01030         0.03860       0.15870     water-low
## 652       0.03600       0.00247         0.03847       0.21570     water-low
## 653       0.00000       0.00000         0.00000       0.72530     water-low
## 654       0.00000       0.00000         0.00000       1.47360     water-low
## 655       0.00000       0.00000         0.00000       0.00000     water-low
## 656       0.09740       0.01020         0.10760       0.00000     water-low
## 657       0.00000       0.00000         0.00000       0.16810     water-low
## 658       0.05350       0.00840         0.06190       0.00000     water-low
## 659       0.00000       0.00000         0.00000       2.13070     water-low
## 660       0.07690       0.00780         0.08470       0.33380     water-low
## 661       0.00000       0.00000         0.00000       0.97320    water-high
## 662       0.00000       0.00000         0.00000       0.00000    water-high
## 663       0.00000       0.00000         0.00000       0.00000    water-high
## 664       0.00000       0.00000         0.00000       0.72560    water-high
## 665       0.00000       0.00000         0.00000       3.73300    water-high
## 666       0.01460       0.00110         0.01570       1.43600    water-high
## 667       0.01500       0.00510         0.02010       0.33210    water-high
## 668       0.00000       0.00000         0.00000       0.70570    water-high
## 669       0.00000       0.00000         0.00000       1.36380    water-high
## 670       0.00000       0.00000         0.00000       2.13170    water-high
## 671       0.03710       0.00000         0.03710       0.51460    water-high
## 672       0.00000       0.00000         0.00000       0.00000    water-high
## 673       0.07280       0.01340         0.08620       2.23580    water-high
## 674       0.00000       0.00000         0.00000       1.02030    water-high
## 675       0.05530       0.00940         0.06470       0.00000    water-high
## 676       0.00000       0.00000         0.00000       0.00000    water-high
## 677       0.08420       0.01230         0.09650       2.82360    water-high
## 678       0.02850       0.00460         0.03310       0.00000    water-high
## 679       0.03330       0.00760         0.04090       0.43680    water-high
## 680       0.00000       0.00000         0.00000       0.13980    water-high
## 681       0.00000       0.00000         0.00000       1.27660     water-low
## 682       0.00000       0.00000         0.00000       0.00000     water-low
## 683       0.00000       0.00000         0.00000       0.00000     water-low
## 684       0.00000       0.00000         0.00000       0.15530     water-low
## 685       0.00000       0.00000         0.00000       1.52910     water-low
## 686       0.00000       0.00000         0.00000       0.40020     water-low
## 687       0.03830       0.00000         0.03830       0.08470     water-low
## 688       0.00000       0.00000         0.00000       0.23920     water-low
## 689       0.00000       0.00000         0.00000       1.07630     water-low
## 690       0.00000       0.00000         0.00000       1.25280     water-low
## 691       0.00000       0.00000         0.00000       0.12860     water-low
## 692       0.00000       0.00000         0.00000       0.00000     water-low
## 693       0.05940       0.00390         0.06330       0.48940     water-low
## 694       0.00000       0.00000         0.00000       1.04530     water-low
## 695       0.00000       0.00000         0.00000       0.00000     water-low
## 696       0.00000       0.00000         0.00000       0.08600     water-low
## 697       0.05310       0.00380         0.05690       2.10530     water-low
## 698       0.05120       0.00950         0.06070       0.00000     water-low
## 699       0.00000       0.00000         0.00000       0.65810     water-low
## 700       0.02370       0.00400         0.02770       0.27220     water-low
recruit[is.na(recruit)] <- 0

recruit[,"eph.rate"] <- recruit$ephedra.emergence/3*100

## Percent of ephedra seedlings becoming established
mean(recruit$eph.rate)
## [1] 9.857143
## Percent of brome seedlings becoming established
mean(recruit$brome.prop.begin)
## [1] 51.36429

Shrub-plant facilitation results

## load plant comp data
plant <- read.csv("data//ephedra.plantcomp.csv")

library(lmerTest)
## 
## Attaching package: 'lmerTest'
## The following object is masked from 'package:lme4':
## 
##     lmer
## The following object is masked from 'package:stats':
## 
##     step
## community measures
plant[,"abd"] <- apply(plant[,9:48], 1, function(x) sum(x, na.rm=T)) ## abundance 
plant[,"rich"] <- apply(plant[,9:48], 1, function(x) sum(x>0, na.rm=T))

## percent brome
plant[is.na(plant)] <- 0
mean(plant[,"B.rubens"]/plant[,"abd"])*100
## [1] 69.22444
## fit a linear model
m1 <- glmer.nb(abd ~ microsite + (1|year) + (1|site), data=plant)
summary(m1)
## Generalized linear mixed model fit by maximum likelihood (Laplace
##   Approximation) [glmerMod]
##  Family: Negative Binomial(9.0118)  ( log )
## Formula: abd ~ microsite + (1 | year) + (1 | site)
##    Data: plant
## 
##      AIC      BIC   logLik deviance df.resid 
##   4883.1   4903.7  -2436.6   4873.1      445 
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.4761 -0.6159 -0.0603  0.5463  3.2187 
## 
## Random effects:
##  Groups Name        Variance Std.Dev.
##  year   (Intercept) 0.003222 0.05677 
##  site   (Intercept) 0.078784 0.28069 
## Number of obs: 450, groups:  year, 3; site, 3
## 
## Fixed effects:
##                Estimate Std. Error z value Pr(>|z|)    
## (Intercept)     4.91598    0.16702  29.433   <2e-16 ***
## micrositeshrub  0.31954    0.03261   9.798   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Correlation of Fixed Effects:
##             (Intr)
## microstshrb -0.098
car::Anova(m1, test="Chisq")
## Registered S3 methods overwritten by 'car':
##   method                          from
##   influence.merMod                lme4
##   cooks.distance.influence.merMod lme4
##   dfbeta.influence.merMod         lme4
##   dfbetas.influence.merMod        lme4
## Analysis of Deviance Table (Type II Wald chisquare tests)
## 
## Response: abd
##            Chisq Df Pr(>Chisq)    
## microsite 95.992  1  < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
m2 <- glmer.nb(rich ~ microsite + (1|year) + (1|site), data=plant)
## Warning in theta.ml(Y, mu, weights = object@resp$weights, limit = limit, :
## iteration limit reached
summary(m2)
## Generalized linear mixed model fit by maximum likelihood (Laplace
##   Approximation) [glmerMod]
##  Family: Negative Binomial(329887.7)  ( log )
## Formula: rich ~ microsite + (1 | year) + (1 | site)
##    Data: plant
## 
##      AIC      BIC   logLik deviance df.resid 
##   1399.3   1419.9   -694.7   1389.3      445 
## 
## Scaled residuals: 
##      Min       1Q   Median       3Q      Max 
## -1.10029 -0.48707  0.01885  0.34541  1.89031 
## 
## Random effects:
##  Groups Name        Variance  Std.Dev.
##  year   (Intercept) 0.0008052 0.02838 
##  site   (Intercept) 0.0374271 0.19346 
## Number of obs: 450, groups:  year, 3; site, 3
## 
## Fixed effects:
##                Estimate Std. Error z value Pr(>|z|)    
## (Intercept)     1.19133    0.11531  10.331   <2e-16 ***
## micrositeshrub -0.57803    0.05999  -9.636   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Correlation of Fixed Effects:
##             (Intr)
## microstshrb -0.177
car::Anova(m2, test="Chisq")
## Analysis of Deviance Table (Type II Wald chisquare tests)
## 
## Response: rich
##            Chisq Df Pr(>Chisq)    
## microsite 92.855  1  < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
### calculate averages and variance
plantavg <- plant %>% group_by(microsite) %>% summarize(ABD=mean(abd), RICH=mean(rich),ABD.se=se(abd)*1.96,  RICH.se=se(rich)*1.96 )

##abundance
abd <- plantavg[,c(1:2,4)]
abd[,2:3] <- abd[,2:3]/0.25

## plot
plot1 <- ggplot(abd, aes(x=microsite, y=ABD, fill=microsite)) + geom_bar(stat="identity", position=position_dodge(width=0.9), color="black") + ylab(expression("plant density (m"^2*")")) + theme_Publication() + geom_errorbar(aes(x=microsite, ymin=ABD-ABD.se, ymax=ABD+ABD.se), position=position_dodge(width=0.9), width=0) + xlab("") + scale_fill_brewer()
## Warning: `legend.margin` must be specified using `margin()`. For the old
## behavior use legend.spacing
## richness
rich <- plantavg[,c(1,3,5)]


## plot
plot2 <- ggplot(rich, aes(x=microsite, y=RICH, fill=microsite)) + geom_bar(stat="identity", position=position_dodge(width=0.9), color="black") + ylab("species richness") + theme_Publication() + geom_errorbar(aes(x=microsite, ymin=RICH-RICH.se, ymax=RICH+RICH.se), position=position_dodge(width=0.9), width=0) + xlab("") + scale_fill_brewer()
## Warning: `legend.margin` must be specified using `margin()`. For the old
## behavior use legend.spacing
require(gridExtra)
## Loading required package: gridExtra
## 
## Attaching package: 'gridExtra'
## The following object is masked from 'package:dplyr':
## 
##     combine
grid.arrange(plot1, plot2, nrow=2)
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database

### compare just brome
plant[,"perBrome"] <- plant[,"B.rubens"]/plant[,"abd"]*100

m1 <- glmer(B.rubens/abd ~ microsite + (1|site) + (1|year), data=plant, family="binomial")
## Warning in eval(family$initialize, rho): non-integer #successes in a binomial
## glm!
summary(m1)
## Generalized linear mixed model fit by maximum likelihood (Laplace
##   Approximation) [glmerMod]
##  Family: binomial  ( logit )
## Formula: B.rubens/abd ~ microsite + (1 | site) + (1 | year)
##    Data: plant
## 
##      AIC      BIC   logLik deviance df.resid 
##    305.3    321.8   -148.7    297.3      446 
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -4.3433 -0.1943  0.0857  0.2643  1.2188 
## 
## Random effects:
##  Groups Name        Variance Std.Dev.
##  site   (Intercept) 2.6488   1.6275  
##  year   (Intercept) 0.6417   0.8011  
## Number of obs: 450, groups:  site, 3; year, 3
## 
## Fixed effects:
##                Estimate Std. Error z value Pr(>|z|)    
## (Intercept)     -0.2411     1.0640  -0.227    0.821    
## micrositeshrub   4.2433     0.4690   9.048   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Correlation of Fixed Effects:
##             (Intr)
## microstshrb -0.099
car::Anova(m1, test="Chisq")
## Analysis of Deviance Table (Type II Wald chisquare tests)
## 
## Response: B.rubens/abd
##            Chisq Df Pr(>Chisq)    
## microsite 81.858  1  < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
m2 <- glmer.nb(B.rubens ~ microsite + (1|site) + (1|year), data=plant)
summary(m2)
## Generalized linear mixed model fit by maximum likelihood (Laplace
##   Approximation) [glmerMod]
##  Family: Negative Binomial(3.1316)  ( log )
## Formula: B.rubens ~ microsite + (1 | site) + (1 | year)
##    Data: plant
## 
##      AIC      BIC   logLik deviance df.resid 
##   4921.8   4942.3  -2455.9   4911.8      445 
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -1.6697 -0.6630 -0.1346  0.5268  2.8941 
## 
## Random effects:
##  Groups Name        Variance Std.Dev.
##  site   (Intercept) 0.26562  0.5154  
##  year   (Intercept) 0.03112  0.1764  
## Number of obs: 450, groups:  site, 3; year, 3
## 
## Fixed effects:
##                Estimate Std. Error z value Pr(>|z|)    
## (Intercept)     4.13618    0.31718   13.04   <2e-16 ***
## micrositeshrub  0.99767    0.05745   17.37   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Correlation of Fixed Effects:
##             (Intr)
## microstshrb -0.093
car::Anova(m2, test="Chisq")
## Analysis of Deviance Table (Type II Wald chisquare tests)
## 
## Response: B.rubens
##            Chisq Df Pr(>Chisq)    
## microsite 301.57  1  < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plant %>% group_by(microsite) %>% summarize(avg=mean(B.rubens), error=se(B.rubens))
## # A tibble: 2 x 3
##   microsite   avg error
##   <fct>     <dbl> <dbl>
## 1 open       82.4  4.02
## 2 shrub     174.   4.95